[gmx-users] Re: GROMACS and Amber FF
michel.cuendet at epfl.ch
Tue Jan 25 15:18:49 CET 2005
>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.
Michel Cuendet, Ph.D. student
Laboratory of Computational Biochemistry and Chemistry
Swiss Federal Institute of Technology in Lausanne (EPFL)
Switzerland Phone : +41 1 693 0324
lcbcpc21.epfl.ch/~mitch +41 1 633 4194
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