[gmx-users] Re: GROMACS and Amber FF
feenstra at few.vu.nl
Fri Feb 4 08:34:01 CET 2005
Michel Cuendet wrote:
>> for my PhD thesis I am working on DNA with GROMACS. You see the problem?
>>> It seems to be better to use Amber FF for DNA simulations. As I read
>>> in the mailing list (1 year ago or so), you are/were working on an
>>> AMBER FF implementation into GROMACS. How far are you? Could I obtain
>>> it from you?
>> Other people have been working on this. Anton Feenstra made a converter
>> from AMBER to GROMACS which requires you to have an AMBER topology. Erik
>> Lindahl and other people in Stanford have worked on a native
>> implementation. I don't know what the status of that is.
> Yes gromacs works with the AMBER ff, BUT you have to correct the BUG
> for tip3p water in version 3.2.1, already described in this list. It's
> an easy fix to files csettle.c and fsettle.f. Otherwise, your water
> will start to flow across your box, and if you stop the water center of
> mass, your protein will be teared apart.
> This should be WRITTEN BIG on the gromacs website in the converter
> download section. By the way, this converter doesn't work for large
> numbers of atoms. We have a better one here, just mail.
I'm actually running some benchmarks with Gromacs/Abmer and Amber/Amber
to see how they compare. (and, boy, isn't amber s-l-o-w-w-w-w....)
* NOTE: New Phone & Fax numbers (below) *
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
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