Sciencemadness Discussion Board

Quantum Chemical Software Available

Sauron - 8-1-2007 at 16:14

I noticed with pleasure that some ab initio quantum mechanical chemistry software is available on the MadHatter ftp site, specifically Gaussian 98W.

I am wondering how many of us in ScienceMadness are interested in such computational chemistry software?

If there is any interest I can upload the excellent V.Lobanov ports of semiempirical MOPAC 6 to the Windows platform. I have three versions: one for 50 atoms, one for 150 atoms and one with NBO program added. Also the manuals by the respective authors.

MOPAC (Molecular Orbital Package) was developed in the 80s By Dr.Stwart of the Michael Dewar group at UT Austin. The ones I am talking about are command line, there is no GUI front end. However they are dead simple to run.

You prepare a standard format input file. Then place it in same directory as the MOPAC executable and run MOPAC with the filename. MOPAC will crunch the file according to the keywords you provided in the input file. And spit out a large output file.

When I started using this a decade or more ago a typical desktop PC would allow MOPAC code to process a typical molecular structure in a fraction of a second to a few seconds. Well, PCs have not slowed down since 1995 have they?

There are later versions of MOPAC but most of the changes reflect solid state applications in keeping with the present employement of Dr Jim Stewart by Fujitsu. One of these versions with a Windows GUI is incorporated into ChemOffice Ultra.

AMPAC now in version 8 was a parallel development from same group and is now sold by Dr Andy Holden Semichem Inc. AMPAC now has a GUI front end and 3D display, and is optimized to be front end for CODESSA a QSPR program also sold by Semichem. These programs are not free but Andy has very liberal policies to academic users. It is also possible to have a trial period for free.

Another readily available Windows port is GAMESS which is an ab initio package maintained by the Gordon Group at Ames. The Windows port is by a Russian chemist at Moscow State University. GAMESS requires a different style of input file than MOPAC GAMESS is free and so is the Windows port and manual.

Let me know if anyone is interested in seeing these uploaded to MadHatter FTP.

chemoleo - 8-1-2007 at 19:37

I think there is decidedly an interest on this. Please check
https://sciencemadness.org/talk/viewthread.php?tid=1437
https://sciencemadness.org/talk/viewthread.php?tid=6299

Although not precisely on the subject matter, there are some additional threads on this which I sadly cant find anymore.

Sauron - 8-1-2007 at 23:07

It has been a little while since I ran MOPAC 6 but I will do so again to verify the procedure.

My recollection is that in the directory where the executable is present, the command line is:

mopac filename.dat

where filename is the actual filename which ought to be significant, such as the compound name.

Control is via the keywords in the first few lines of the input file. The keywords are detailed in the manual. Sample files are also provided. The input files are just ASCII and can be prepared in Notepad. They can also be geberated by some other software such as PC MODEL. I have also used Babel and WinBabel to convert other files such as Brookhaven PDB files to MOPAC input, although the keywords still have to be selected and typed in manually.

The GUI interfaces for later versions are really just ways to input keywords.

I will be happy to upload the three MOPAC 6 executables I have on hand. There are other ports of Mopac 6 out there but I tried several and I found Viktor Lobanov's ports to be the fastest most efficient ones. The differences all have to do with the selection of compiler.

And I will upload the manual as well.

I will investigate the current status of PC GAMESS and if I can obtain that again and the documentation I will also upload it. Note that as an ab initio package GAMESS requires basis sets (just as Gaussian does) while the semiempirical MOPAC (and AMPAC) do not.

It has been a while since I looked at Gaussian 98W but my recollection is that due to speed and memory limitations in PCs at the time it was done (almost a decade ago) it has some fairly serious limitations as to number of atoms in a molecular structure to be studied. A pity because obviously the computer constraints have been greatly ameliorated since then (RAM, CPU speed, hard disk space issues.)

As soon as I upload I will post again and announce.

Sauron - 9-1-2007 at 22:45

PC GAMESS

"General Atomic & Molecular electronic Shell Structure" is what GAMESS stands for is I recall

Here is the url for the website of this freely distributed ab initio quantum-chemistry package from Iowa State University and Moscow State University:

http://classic.chem.msu.su/gran/gamess/

Note that there are three or four seperate GUI front ends available for ease of use, and all but one are also free of charge.

Full documentation is available as well as sample input files.

An obline tutorial is available.

Currently in version 7.0

[Edited on 10-1-2007 by Sauron]

[Edited on 10-1-2007 by Sauron]

Sauron - 10-1-2007 at 14:52

MOPAC 6 software and manuals, also NBO 3

I just uploaded three folders to MadHatter's ftp site:

mopac6nbo3

mopac50v6

mopac 150v6

Each folder contains a MOPAC 6 executable (.exe) file along with a small sample input file ethylene.dat and a mopac manual in ASCII txt.

In addition the mopac6nbo3 folder contains the NBO 3 manual in html

50 and 150 refer to the maximum number if atoms in molecules under study (50 atoms/100 hydrogens, or 150 atoms 200 hydrogens.)

These are fortran codes ported to run under 32 bit Windows at the DOS prompt.

To run MOPAC, you type mopac filename.dat then enter.

MOPAC will crunch the file and spit out several new files, an .arc file, a .end file, a for011 file, and the main output file with extension .mno or .out.

All of these will have same filename as the input file, just the extensions will be different.

You can try it with the ethylene.dat file, that is what it is there for.

The output file is many pages of data, you can read it on screen by using the type (filename.xxx)|more command, page by page.

Or you can print it out if you are not a tree hugger.

Source code is available.

Enjoy!

[Edited on 10-1-2007 by Sauron]I am still looking for a freely distributed GUI front end for MOPAC 6 and will upload it if I find it.

[Edited on 10-1-2007 by Sauron]

Polverone - 10-1-2007 at 21:05

Coincidentally, I just received the following in my email:
Quote:
Dear NWChem users,

On behalf of the High Performance Software Development group at EMSL
you are cordially invited to attend a two-day meeting on January 25-26
that the Environmental Molecular Sciences Laboratory (EMSL) is
organizing to develop a long-term strategy for EMSL's NWChem quantum
chemistry software suite.

Participants at the meeting will provide input and ideas as to what the
future computational chemistry scientific challenges will be, which role
petascale computing will play and how it can be achieved, and the most
significant needs in terms of capability development in NWChem. In
addition, discussions will be held regarding the possibility of NWChem
going open-source and the development of a NWChem developers consortium,
enabling the development of a broader developer base.

The meeting will include scientific leaders in key programs and science
areas along with key computational chemistry methodology developers,
computer scientists, and mathematicians and is open to the scientific
community. Invited speakers are: ...

There are more than a few interesting things about NWChem. For one thing, it is one of the most modern quantum chemistry code bases in general use, which makes collaborative development more likely should it be open-sourced.

For another thing, it is extremely scalable. When I was at PNNL I could regularly see NWChem jobs running on the massively parallel system using 500-1000 (sometimes 1000+!) processors. You can see some rather dated benchmarks illustrating scaling here; they are quite impressive compared to (e.g.) Gromacs or Gaussian, though the MD side probably isn't quite as scalable as NAMD. Why should you care, if you don't have a building full of rackmounted compute nodes? Intel and AMD seem to be in a "core race" similar to the old megahertz race. Only scalable parallel software can get full benefit from the explosion of cores on the desktop, and NWChem is the very image of scalable parallel chemistry software.

NWChem's input format is nice. To do serious work with any quantum chemistry package I've used, you eventually have to type out textual input or write a program to automate the input generation, but as such things go I think NWChem has a clearer, more forgiving, less legacy-burdened input style than GAMESS or Gaussian.

NWChem implements a wide variety of methods, some of them quite advanced, and it is unusual in using automatically generated code to implement some of its advanced post-Hartree-Fock methods. The Tensor Contraction Engine, bundled with NWChem, accomplishes this and is a small marvel in itself.

In addition (and unlike GAMESS US or MPQC), NWChem is well-funded and has a large, active group of developers at PNNL and a few collaborating institutions. If it were to go GPL, as MPQC did, or even to appear under another open source license, I would be delighted.

Any amateurs who indulge in computational chemistry should likewise be excited by the prospect. With access to high quality software like NWChem and PC GAMESS, one very rarely has to consider buying Gaussian or trying to pirate it. Theoretical/computational chemistry lack the sensual thrills of amateur bench chemistry, but they have just as much (if not more) potential for motivated individuals to do genuinely new work. Good tools are inexpensive and widely available, there are no regulatory barriers, and you don't need much space to work. I would encourage every serious amateur to learn a bit about computational chemistry; it's one of the few areas where we have an advantage over amateurs who were working 50 years ago.

pantone159 - 10-1-2007 at 22:13

Quote:
Originally posted by Polverone
Any amateurs who indulge in computational chemistry should likewise be excited by the prospect. With access to high quality software like NWChem and PC GAMESS, one very rarely has to consider buying Gaussian or trying to pirate it.


That is indeed very exciting. I've never done any computational chemistry, although I have done a lot of programming and numerical methods stuff. I have downloaded PC-GAMESS, but I haven't been brave enough to try and construct any input files. (Are there tools for this? That would help.)

From a philosophical point of view, having a solid, free competitor to Gaussian is fabulous. I understand that Gaussian restricts its use by some scientists (and even whole departments), who for example criticize them. In Science, that sort of attitude is repugnant and unacceptable. The tools of knowledge must be available to all.

Sauron - 10-1-2007 at 22:22

I think we enjoy this advantage over professionals working 50 years ago or even 25 years ago. I remember with great clarity how it was in the 70s. RA's, grad students and postdocs had to prepare paper tapes and punchcards to run on PDP-11s or go pay some serious obeisances to the lords of the departmental mainframe to get timesharing. Even the older codes we are talking about like MOPAC and GAMESS did not exist. Comp-chem was just in its teething stages. What professional had the sheer computing power we now take for granted on our personal desktops or laptops, merely a quarter of a century ago?

It is mind boggling.

Add to that the ability to have a pretty good chemistry library at hand on the desktop at no cost (so that one's $$$ can go for reagents and glassware like it ought to and one's time spent at the bench rather than at the library). In the site library and on the ftp sites we have the library resources of a senior professor who has been subscribing to 3-4 major journals for 30-35 years and hoarding every issue plus accumulating books. A junior prof wouldn't even have that, it takes time. Decade after decade.

But not for us. All we have to do is download it. It costs a little time and effort. Days not years, weeks not decades. Maybe a month noit a lifetime.

Sauron - 10-1-2007 at 23:10

@pantone159, I was unaware that Gaussian was that hegemonistic. I'd like to hear more about that.

Indeed there are at least four GUI front ends (tools for preparing input files and running PC GAMESS). And three of them are freely downloadable. The fourth has a free crippleware version, plus a trial version that is full featured and works for 60 maybe 90 days. Pricing is inexpensive, $120 academic $190 commercial so it is hard to kvetch.

All these are detailed on the PC GAMESS home page at Moscow State Univ., see link in my post above.

I started playing with PC GAMESS about 10 years ago and none of these GUIs existed at that time.

Another tool for comp chemists is BABEL (DOS) and its Wintel variant WinBabel. This is a file format conversion utility. I think I will upload it to MadHatter.

Polverone - 10-1-2007 at 23:10

Quote:
Originally posted by pantone159
That is indeed very exciting. I've never done any computational chemistry, although I have done a lot of programming and numerical methods stuff. I have downloaded PC-GAMESS, but I haven't been brave enough to try and construct any input files. (Are there tools for this? That would help.)

From a philosophical point of view, having a solid, free competitor to Gaussian is fabulous. I understand that Gaussian restricts its use by some scientists (and even whole departments), who for example criticize them. In Science, that sort of attitude is repugnant and unacceptable. The tools of knowledge must be available to all.

There are various tools and frontends that work in conjunction with PC GAMESS.
RUNpcg seems to be a loose collection of frontends that will work with other molecule builders and PC GAMESS (this appears to be an updated version of PCGam).

Facio appears to have more integrated capabilities for modeling and molecular docking too.

Chemcraft costs some money ($105) but offers maybe more capabilities than Facio, and interfaces with multiple codes.

The above programs were suggested by Sauron. I have not used them.

The one program I have used, Gabedit, is free and offers a graphical user interface molecule builder/visualizer with many preset options plus a script editor. It interfaces with GAMESS, Gaussian, Molcas, Molpro, and MPQC. It will remotely execute and monitor jobs, so (for example) you can build an input structure on your Windows desktop at home, execute it on a campus departmental server, and watch the course of the geometry optimization as the program executes.

I think that all of these programs except RUNpcg will need a little coaxing for use with PC GAMESS. The PC GAMESS input has a few different options from GAMESS US, which probably doesn't matter unless you need to use advanced features, but the output format is different enough that (for example) the programs probably won't visualize an electrostatic potential cube file as output by PC GAMESS.

If you want to visualize results, you will probably need to use an existing conversion tool or write your own, to make PC GAMESS output follow GAMESS US format.

GAMESS US is a fine program in its own right, but I prefer PC GAMESS for its superior performance and slightly cleaner command line operation. Still, you will not go wrong starting with GAMESS US and a graphical frontend to save you some time poking through manuals. You'll read the manuals eventually, of necessity, but need not deal with them immediately.

I know that some members here are interested in unusual phenethylamines, tryptamines, and other mind-bending chemicals. Want to determine which ones have the most promise of interesting biological activity before you consume expensive reagents and risk legal trouble? Get models of the receptors you're interested in from the Protein Data Bank, geometry-optimize and parameterize the molecules of interest, then do docking/binding studies with the receptors. True, this takes time, and the docking software itself seems to be a weak link (harder to find freely available docking code than general quantum or MD software), but it is a powerful tool regularly used in academia and industry. And you can do it with a computer no more powerful than the one you use to browse Sciencemadness.

Edit: I forgot to mention that Gaussian Inc. are truly jealous and run counter to the general scientific ethos when it comes to protecting their quantum chemistry software market. John Pople, the original author of Gaussian who spent more than 15 years on it and won the Nobel Prize for his contributions to theoretical chemistry, is legally barred from using Gaussian software because he now works on competing programs. Any students or post-docs of his are likewise barred. See Banned by Gaussian for a more thorough account of people and institutions who are blacklisted by Gaussian.

Gaussian is a de facto standard among computational chemistry users, but it doesn't need to be privileged that way. Use free software, and invest the savings in better hardware, or chemicals, or a nice meal -- just don't buy Gaussian unless you really must.

[Edited on 1-11-2007 by Polverone]

Sauron - 10-1-2007 at 23:23

ChemCraft Software - A GUI front end for PC GAMESS

http://www.chemcraftprog.com/

Free trial fully featured version (several months)

Free "slightly crippled" version

Inexpensive pricing in $100-$200 range.

Sauron - 10-1-2007 at 23:32

FACIO freeware GUI front end for PC GAMESS and GAUSSIAN

http://www1.bbiq.jp/zzzfelis/Facio.html

See this website to believe it and it is FREE!

Sauron - 10-1-2007 at 23:44

I would say that blacklisting the Nobel winner who created the program they now flog, places Gaussian Inc. beyond the Pale as far as I am concerned.

I might use their software but never give them one thin dime for it.

While I am not an admirer of Abbie Hoffman I will paraphrase him and recommend that you "STEAL THIS SOFTWARE!"

Sauron - 10-1-2007 at 23:50

Caveat: I have not yet used any of these GUIs for PC GAMESS but I have installed most of them and will try them all once I get PC GAMESS 7.xx installed.

All of these m.o. packages have idiosyncratic input files, keywords and conventions and except for AMPAC/MOPAC not a lot of commonality.

It should be noted that input formats require a certain rigor in preparation and proofing or these programs will barf all over them. Searching out a simple error can be tedious. Remember you need to use a plain text editor (like Norepad) and NOT a word processor.

Sauron - 10-1-2007 at 23:58

RUNpcg Scripts (GUI front end for PC GAMESS)

http://dcbwww.unibe.ch/groups/schumacher/qc/RUNpcg.htm

Freeware!

Sauron - 11-1-2007 at 00:05

@Polverone, I thank you for the clickthrough to Gabedit.

I will give it a try.

I do not know why Alex Granovsky omitted it from his section on PC GAMESS Gui front ends on the PC GAMESS site (q.v.)

The PCGam page appears to just refer one on to the RUNpcg page, so I guess they are integrated.

If so that still leaves us with four PC GAMESS Guis, three of them free.

RUNpcg
Facio
Gabedit

and the not quite free

ChemCraft

Why not try them all?

Sauron - 11-1-2007 at 00:15

BTW the GaussView front end for GAUSSIAN and Gaussian98W was written by Dr Andy Holder of Semichem and is essentially the same molecular builder as AmGui his front end for AMPAC which he maintains of course, being a veteran of the Dewar Group at UT Austin where both AMPAC and MOPAC originated.

Andy Holder is a very nice guy and is very friendly to all who are interested in comp-chem.

He also sells CODESSA which is my personal fave. QSPR/QSAR.

While Alan Katritzky has stated that its successor CODESSA PRO will not be sold to "home users" which rather irked me. CODESSA PRO is not sold through Semichem.

[Edited on 11-1-2007 by Sauron]

Sauron - 11-1-2007 at 00:36

@Polverone, according to the Gabedit site you linked to,:

"For Windows users, please note that Gabedit work with WinGamess but not with PCGamess. '

Which certainly explains why it was absent from the PC GAMESS page.

I don't know anything about WinGAMESS as yet but I did notice that PCGamess had side by side benchmarks with WinGAMESS on same hardware and beat it handily.

So now I will go look into WinGAMESS

Answers: see http://www.msg.ameslab.gov/GAMESS/dist.pc.html

There are FIVE different versions of GAMESS US compiled for PC, of which PC GAMESS from Moscow State Univ. is the only one which has been tested by Ameslab (Iowa State) Gordon Group. Furthermore Gordon Group has not a single PC running Windows. All their PCs are MAC OS x or Red Hat Linux. Therefore the Gordon Group cannot and will not answer any questions nor provide any support for any GAMESS under Windows.

It is pretty clear that they distance themselves from all such implementations except for PC GAMESS which ought to be suggestive to us all.

Anyone know of any freely available or pirated GUI for MOPAC 6?

Later versions of MOPAC have GUI front ends but are invariably owned by Fujitsu and are expensive. Furthermore almost all improvements over version 6 seem to focus on solid state (MOSOL) calculations. Which is great for the materials scientists but not very interesting for me.

[Edited on 11-1-2007 by Sauron]

Sauron - 11-1-2007 at 01:37

And @Polverone, I note with sadness the following notice on the NWChem website:

Please Note: In order to obtain NWChem, you must be a permanent faculty or staff member of the facility or institution you are associated with. We can NOT accept User Agreements from students or post docs.

SO: NWChem is not available to amateurs at all. Not even US citizens inside the US. Permanent faculty and staff of institutions. I'd say that lets most of us out.

Furthermore this is source code that must be ported to run on Windows, rather than being a precompiled executable. For non programmers this adds appreciably to the learning curve.

Finally while the advent of petascale computing for quantum chemistry is indeed thrilling I do not see how amateurs are likely to avail themselves of massively parallel computer systems. That is not cost free. I thought the object of amateur involvement in computational chemistry was to avoid the costs of chemicals and apparatus and equipment, not to replace one money pit with a silicon money pit.

NWChem is interesting but I just don't see how it fits in with my interests in computational chemistry the way that some of these other packages do.

Or did I miss something in that announcement you posted?

And I can certainly see why this would be particularly exciting for someone embroiled in biological macromolecules research.

[Edited on 11-1-2007 by Sauron]

Polverone - 11-1-2007 at 10:05

The announcement that I copied (see bolded part) (suggests that the developers are considering open-sourcing NWChem, i.e. dropping the highly restrictive licensing and allowing other people to work with and on it.

None of us can afford massively parallel systems at this time, but the projected roadmap for increased performance from desktop processors over the next few years seems to call for increasing parallelism. As the number of cores on your machine goes up, the scalability of your software becomes more important, and NWChem is highly scalable.

I'm not suggesting that amateurs buy and install their own HPC cluster in a miniature home data center. I'm suggesting that today, $2000 spent on desktop hardware purchases 2-4 cores. 5 years from now that may be 8-16 cores. Actually, though it seems unlikely to see general use, Intel has already fabbed a massively parallel, 80 core, teraflop-on-one-chip processor and it seems that their future plans do involve continual increases in parallelism. At some number of cores/processors I believe PC GAMESS will be unable to continue scaling efficiently (at least not without substantial developer effort), while initially-slower codes like MPQC and NWChem will continue to scale, meaning they'll eventually show higher performance on desktop machines with large numbers of cores.

Finally, although it may not run as well on Windows, NWChem does run on that platform and if it's open-sourced I'm sure there will be somewhere for people to download precompiled binaries for their platform.

Sauron - 11-1-2007 at 14:29

@Polverone, thanks, and I hope you are right. PNNL is after all a federal lab and the present administration is not too keen on giving away very advanced scientific software. The announcement indicated that the subject of open sourcing would be discussed at the Jan 25/26 meeting, not that it was a done deal, and not exactly how it might be implemented. After all they are distributing source code now. '

I do take your point about increased parallelism in the immediate future (1-10 years) and the normal rule of thumb is what? Twice the power for half the price every year or two. Extrapolate.

Sauron - 11-1-2007 at 14:34

I found a couple of third party freeware developments based on MOPAC that provide a GUI front end on Windows platform.

WinMOPAC 7.21 from a Russian academic team

and MoCalc from a Brazilian academic team. This one also is a front end for one version of GAMESS or another.

I will investigate and post here.

Polverone - 11-1-2007 at 15:24

Quote:
Originally posted by Sauron
@Polverone, thanks, and I hope you are right. PNNL is after all a federal lab and the present administration is not too keen on giving away very advanced scientific software. The announcement indicated that the subject of open sourcing would be discussed at the Jan 25/26 meeting, not that it was a done deal, and not exactly how it might be implemented. After all they are distributing source code now.

I'm not sure how much impact the current administration at the top would have this far down, and in any case it only has a couple more years. If PNNL can take NWChem and make it open source, then they get:
1) a larger user base
1a) more NWChem literature citations from those new users
2) (potentially) more developers who would contribute features without being employed by PNNL -- I personally would be guarded about this because the number of good theoretical chemists who are also good programmers and have time to work for free is probably small (bugfix contributions might be realistic, though)

1 and 1a are the most important points in my mind, even though "open source" usually brings up images associated with point 2. At the end of the year administrators have to be able to show how funds spent in their department contributed to PNNL's scientific mission. Changing NWChem's licensing would negligibly affect its development/distribution costs while potentially expanding its user base, and hence scientific impact, quite considerably. Apart from administrators, I'm sure the developers themselves would like to see their work receive as much recognition and use as possible.

If someone's trying to pick a computational chemistry suite, it's easier to try (and maybe stick with) a package that you can just click and download than one which requires registration with a signed and approved license form.

MPQC was developed by Sandia and it's completely open, GPL'd and available from Sourceforge like every other program there. GAMESS US is developed by Ames Laboratory, and while it's not as free as MPQC, it's still available after only a token registration process. NWChem is a weird holdout, even among programs developed by national laboratories, in its extra-strict licensing. I hope and have reason to think that may change.

NWChem's greatest strength, compared to MPQC and GAMESS US, is its constant in-house use and development at PNNL. Last year I met a developer who was working for the summer on NWChem, and he said that he could have worked on MPQC or GAMESS that summer, but MPQC struggled for funding and GAMESS was a pain to work with because it's been mostly developed by a long string of post-docs and students who work on it for a few years then go elsewhere. NWChem has a stable user and developer community at PNNL and its development goes hand-in-hand with new hardware evolution.

[Edited on 1-11-2007 by Polverone]

Sauron - 11-1-2007 at 15:59

Yeah but GAMESS (and AMPAC/MOPAC) were 1980s codes originally, I don't know about the one from Sandia. MOPAC 6 was done while Jim Stewart was at the USAF Academy (teaching) and that's why it is public domain. (The USAF makes that very clear in the intro to the manual).

I do hope you are right. I'll be happy to see NWChem freely available.

Meanwhile I just uploaded to the MadHatter FTP site, WinMOPAC 7.21 which is a GUI implementation of MOPAC 7 by PSU (Perm State University, Russian Federation). The installation package is only 1 Mb and includes RasWin.

As a companion to this I also uploaded Dr Jeff Gosper's BabelWin applet, a file conversion utility for computational chemistry and molecular modelling formats. Jeff and I used to correspond when he was at Brunel Univ. in the UK, later he went with Tripos, I don't know his present whereabouts. He was the creator of ReView, a neat visualization tool for molecular vibration modes. I recommend it.

The url for the home page of this program is
http://www.psu.ru/science/soft/winmopac/index_e.html

This is freeware. Pending a closer look I will go out on a limb and say that this is AFAIK as close as you can get for free to MOPAC 2000 or MOPAC2002 from Fujitsu

Looks like you start with a Brookhaven PDB file (Protein Data Base) and go from there. This is basically the way I was doing it at the command line a decade ago but I would really have loved to have had a GUI at that time. So, enjoy.

It's all about choices. Ab initio vs semiempirical, and then a veritable Baskin-Robbins of flavors and topings of each after that. Find one you like. The number of free packages is much larger than it was a decade ago.

[Edited on 12-1-2007 by Sauron]

Sauron - 11-1-2007 at 18:15

MOCALC 2.2 a Freeware GUI Front End for Both MOPAC 6 and PC GAMESS

http://www.cce.ufes.br/anderson/mocalc.html

I have combined the setup file, the manual and a copy of the authors' article in the Journal of Computational Chemistry into a zip file and will upload to MadHatter FTP forthwith.

This is the slickest GUI I have seenm and it bridges the gulf between the ab initio and the semiempirical MO packages very neatly by combining a graphical user interface front end with utilities for file import, conversion and editing for both MOPAC 6 (which is included) and PC GAMESS (which the user must obtain from the Gordon Group then place in appropriate directory per instructions provided in MoCalc.)

Like some other GUIs it employs the familiar tools Babel and RasMol as helpers. But it also is a front end for TINKER, about which I know nothing as yet.

If you only want to have one GUI front end this is the solution.

And it is free.

[Edited on 12-1-2007 by Sauron]

Sauron - 11-1-2007 at 18:24

In summary we now have available not only Gaussian 98W, but also several GUIs for PC GAMESS (which itself is free from the Gordon Group at Ameslab); three command line ports of MOPAC 6 to run under 32 bit Windows; WinMOPAC 7.21; and now MOCALC 2.2 front end for both MOPAC 6 (built in) and PC GAMESS (easy add-on) as well as TINKER.

Executables are either uploaded to MadHatter or are linked to websites found in this thread, q.v.

Happy crunching!

Sauron - 12-1-2007 at 19:22

TINKER Tools for Molecular Design

http://dasher.wustl.edu/tinker/

is the TINKER Home Page. This package (along with MOPAC 6 and PC GAMESS) in integrated into MOCALC 2.2 or it can be used as a standalone by downloading from the site linked above, which is Washinton University in St.Louis Missouri.

TINKER is free

[Edited on 13-1-2007 by Sauron]

[Edited on 13-1-2007 by Sauron]

Ghemical and associated Linux tools

Polverone - 12-1-2007 at 21:01

Ghemical is a free, graphical tool for Unix/Linux that offers molecular modeling, conformational search, geometry optimization, ESP visualization, and more with your choice of TRIPOS force field, semiempirical methods through MOPAC7, or ab initio methods through MPQC. If you use Debian or a derivative like Ubuntu, installation is as simple as selecting it in your package manager and performing an update. Otherwise, installation can be a bit of a pain; I was unable to get the MOPAC7 part to properly compile when I tried to assemble it by hand on Redhat 9 system.

Ghemical-GMS is a Ghemical derivative that interfaces it with GAMESS US. If you are uncomfortable installing software under Unix/Linux or trying to find Windows ports of Unix/Linux software, the bootable Vigyaan/GAMESS disk comes with those packages and many more oriented to biochemical research, all ready to run on your PC without any installation or previous knowledge of Linux required.

Sauron - 12-1-2007 at 21:37

The Vigyaan CD was one of the four GAMESS ports that the Gordon Group described as "untested at Ames" and they gave the distinct impression that they were holding their nose.

The MSU Granovsky PC GAMESS is the only one that the AlesLab people who maintain GAMESS US cooperate with.

I am not saying there's anything wrong with the Vigyaan CD ahd I do not automatically knwtow to Iowa but, when in Rome...

Sauron - 12-1-2007 at 21:43

There is a pile of chemical software for Linux, precompiled or in source. I don't work in Linus so have no experience with these.

I wonder if we took a poll of the forum how many Linux users vs Windows users would pop out?

It's not a brand war, I loathe Microsoft and everything they stand for but I use them anyway, and have for 20 years, gritting my teeth all the while.

Polverone - 13-1-2007 at 00:00

If you're interested in the pile of chemical software for Linux but don't want to risk messing up your computer with an installation, there are two options. One is to download/order a bootable CD that is designed to run without installation; you can save your work to a USB flash drive or external hard drive. Another option, which will let you run a bootable CD or a more typical Linux installation, is to download the free VMWare Player or Virtual PC 2004 and install your software inside a virtual machine. Performance is somewhat degraded compared to running on bare hardware -- 3D display speed takes a hit especially -- but it can be a relatively effortless, extremely safe way to sample the offerings under Linux.

Linux was and still can be a huge pain to get configured properly or to install software under (though it does not suffer from Windows' mysterious deterioration over time); for that reason I'd never actively encourage people to abandon Windows for it, unless they had a strong preexisting motivation. I've found the few bootable CDs I've tried to work painlessly and effectively, though, and if you try (e.g.) Ubuntu as I suggested in the previous post, software installation for many useful scientific packages is easier than it would be under Windows. Most computational chemistry software has been running under a Unix longer than under Windows, if it runs on Windows at all, and tends to be better-tuned for Unix/Linux. This doesn't matter much when you are just learning but it becomes significant as your runtimes stretch into hours and days.

Sauron - 13-1-2007 at 01:31

I remember a decade or more ago discussions on the CCL and QCPE (Computational Chemistry List, Quantum Chemical Program Exchange) and also on Alex Granovsky's PC GAMESS sdite and forum about the "best" OS for porting of these old Fortran codes.

The upshot was that there existed a strong prejudice in comp chem circles and perhaps generally in science against Windows and in favor of Linux, the prejudice was not based on performance but on the proposition that all software and all supporting tools such as compilers ought to be free. Linux compilers were free and Windows compilers were not. The Granovsky team however argued very forcibly and persuasively that free does not necessarily mean better. They demonstrated that PC GAMESS compiled under Linux ran much slower on same hardware and processing same input that it did when compiled under Windows NT (at the time I think it was still 3.51 and PC GAMESS was 2.x IIRC).

This made me disfavor my own experimentation with Linux. In the end while I obtained Fortran Power Station 5 and still have it, taught myself Fortran for the second time (I learned a bit previously at the university) and messed aroud compiling MOPAC and AMPAC -- i never completed my GUI project and just used the Lobanov ports of MOPAC 6 under Windows 95, 98 and XP Pro. Never Linux. Same with PC GAMESS.

Windows registry gets bloated over time, it is a periodic chore to clean it out and remove detritus. Same goes for the temp files and internet cache. And staying free from malware of all sorts is a hassle. But there are tools for all of that and in my experience if you use them right the system does not slow down. I am presently running on this machine one HDD under XP SP1 and another under XP SP2 (forced to upgrade by Acrobat Pro 8). Normally there's a second machine netweorked to this one running two drives with XP SP1. Then there are four more machines running 98 that are dedicated to Millenium32 V3.2 Chromatography Manager to run IEEE-488 buses to Waters hardware. These machines have no internet connectivity because the Millenium installations are all pirated and would otherwise phone home to the Waters server. So I am running half a dozen boxes at present under various Windows flavors, my personal experience with Windows dates from old version 3.0 (may it burn in hell along with Bill G.) amd a good many years on 3.1 and 3.11 for Workgroups. 95 was much better, 98 oK, I held onto 95/98 till switching to XP Pro, bypassing 2000, Millenium and NT, NT was tempting though. I am not at all tempted by Vista and will resist migration as long as I can. I'm contrary that way. All in all I've been a prisoner of Microsoft for about 20 years and I guess I am suffering from institutionalization with it. I don't want to be liberated. Tried Netscape and didn't like it. Have resisted all temptation to try Firefox.

I suspect from reading the latest Granovsky material that good compilers now exist for Linux. But I am set in my ways for better or for worse. Something would need to be extraordinarily attractive for me to be motivated to compile it myself, I'd want to hold out for a precompiled executable.

Reference Information

solo - 24-1-2007 at 02:15

High performance computational chemistry: An overview of
NWChem a distributed parallel application
Ricky A. Kendall ; , Edoardo Aprà , David E. Bernholdt , Eric J. Bylaska ,
Michel Dupuis , George I. Fannb, Robert J. Harrison , Jialin Ju , Jeffrey A. Nicholsb, Jarek Nieplocha , T.P. Straatsmab, Theresa L. Windus , Adrian T. Wong
Computer Physics Communications 128 (2000) 260–283



Abstract
NWChem is the software package for computational chemistry on massively parallel computing systems developed by the High Performance Computational Chemistry Group for the Environmental Molecular Sciences Laboratory. The software provides a variety of modules for quantum mechanical and classical mechanical simulation. This article describes the design and some implementation details of the overall NWChem architecture. The architecture facilitates rapid development and portability of fully distributed application modules. We also delineate some of the functionality within NWChem and show performance of a few of the modules within NWChem.

Attachment: High performance computational chemistry- An overview of NWChem a distributed parallel application.pdf (866kB)
This file has been downloaded 1021248 times

NWChem 6.0 now released, and it's open source

Polverone - 1-10-2010 at 10:55

It took 3 years, but NWChem's new 6.0 release is now open source. It can be found at nwchem-sw.org. Previous versions were also distributed as source code but were only available to permanent faculty or staff members of institutions (not students or post-docs).

Why might you choose NWChem over or in addition to GAMESS, Firefly, or MPQC?

-It has well maintained, organized, and fairly easy to read documentation.
-Its input format is more forgiving and (IMO) readable than GAMESS derivatives, or Gaussian, for many tasks.
-It offers methods that may be missing from alternative packages, like plane wave DFT, high-order coupled cluster calculations, molecular dynamics/mechanics, and hybrid MD/QM simulations.
-Many analysis tasks and customizations are possible using the embedded Python interpreter, instead of external programs.
-It scales efficiently to very large processor counts if you have a sufficiently fast interconnect. Admittedly this isn't a big issue for hobbyists.
-Unlike GAMESS and Firefly, it can be downloaded immediately without any registration or approval.
-You are trying to reproduce prior work, and the authors used NWChem.

Why might you choose GAMESS, Firefly, or MPQC over NWChem?

-They offer methods missing from NWChem, like MP4 calculations or alternative internal coordinate schemes.
-They are faster for some calculations, particularly those performed on a single PC.
-Third party software may have interfaces for these packages but lack NWChem support.
-You are trying to reproduce prior work, and the authors used one of the above packages instead of NWChem.
-Ready to use software packages are available for your platform, but NWChem isn't (NWChem prebuilt binaries only available for x86 OS X and Red Hat Linux at present).

NWChem also has a tightly integrated graphical environment for visualizing, preparing, and analyzing calculations called ECCE. ECCE is unfortunately still under a restrictive license, but the NWChem release gives me hope that it too will become open source in the future.

Nicodem - 2-10-2010 at 09:52

Does this one have a beginner friendly interface, anything visual and intuitive at all? If it does not, it still remains for professionals only. If it is only half as horrid for setting up any calculation as is Gaussian or the like, it is not really suitable for anyone but those who have been trained to use it - so no gain for the amateurs.
Anyway, could I use it to calculate the rotational barriers?

madscientist - 2-10-2010 at 13:28

I've never dug into the computational side of chemistry but this is interesting - too bad about the license for ECCE, though.

"Once you have electronically agreed to the EMSL Software User Agreement, your request will be routed for review and approval. This review may take a couple of days..."

That last part doesn't bode well for the odds of success in the "I am a Nobel Prize winning professor at Cal-Tech who just happens to prefer gmail" route.

Anyone try anyway? :D

Polverone - 2-10-2010 at 15:55

Quote: Originally posted by Nicodem  
Does this one have a beginner friendly interface, anything visual and intuitive at all? If it does not, it still remains for professionals only. If it is only half as horrid for setting up any calculation as is Gaussian or the like, it is not really suitable for anyone but those who have been trained to use it - so no gain for the amateurs.
Anyway, could I use it to calculate the rotational barriers?


ECCE is a pretty friendly interface with tight integration, unfortunately as I mentioned ECCE is still very restricted in availability as NWChem itself used to be. It is possible to self-teach even with no graphical interface, but I wouldn't recommend it. It can be used to calculate rotational barriers but if you look at your other thread I think there is an easier solution there :)