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Sauron
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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!
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Sauron
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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]
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Polverone
Now celebrating 21 years of madness
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Ghemical and associated Linux tools
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.
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Sauron
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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...
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Sauron
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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.
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Polverone
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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.
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Sauron
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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.
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solo
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Reference Information
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 1123788 times
It's better to die on your feet, than live on your knees....Emiliano Zapata.
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Polverone
Now celebrating 21 years of madness
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NWChem 6.0 now released, and it's open source
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.
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Nicodem
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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?
…there is a human touch of the cultist “believer” in every theorist that he must struggle against as being
unworthy of the scientist. Some of the greatest men of science have publicly repudiated a theory which earlier they hotly defended. In this lies their
scientific temper, not in the scientific defense of the theory. - Weston La Barre (Ghost Dance, 1972)
Read the The ScienceMadness Guidelines!
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madscientist
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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? 
I weep at the sight of flaming acetic anhydride.
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Polverone
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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 
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