[gmx-users] Re: water molecules in vacuum simulation

[David Mobley]

This may be naive, but have you defined POSRES_WATER, i.e. in your top
or mdp file? If not, the position restraints will be unused.



On 9/28/06, anwar at cdfd.org.in <anwar at cdfd.org.in> wrote:
> Hi all,
> I am facing a problem in constraining the crystallographic water molecules
> during invacuo simulation. Even after including the oxygen atom numbers
> in the .top file for position restrain (given below), the dynamics is going
> the same way as it was without positoion restrain. Please Help me out of
> this.
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
> 12448   1       1000       1000       1000
> 12451   1       1000       1000       1000
> 12454   1       1000       1000       1000
> 12457   1       1000       1000       1000
> 12460   1       1000       1000       1000
> 12463   1       1000       1000       1000
> 12466   1       1000       1000       1000
> 12469   1       1000       1000       1000
> 12472   1       1000       1000       1000
> 12475   1       1000       1000       1000
> 12478   1       1000       1000       1000
> 12481   1       1000       1000       1000
> 12484   1       1000       1000       1000
> 12487   1       1000       1000       1000
> 12490   1       1000       1000       1000
> 12493   1       1000       1000       1000
> 12496   1       1000       1000       1000
> 12499   1       1000       1000       1000
> 12502   1       1000       1000       1000
> 12405   1       1000       1000       1000
> #endif
>
> regards
> Anwar
> ----------------------
> Mohd Anwaruddin
> Project Assistant
> C/o DR.H.A.Nagarajaram
> Lab of Computational Biology and Bioinformatics
> Center for DNA Fingerprinting and Diagnostics(CDFD)
> Nacharam
> Hyderabad-500 076
> INDIA.
> Tel: +91-8413-235467,68,69,70 ext 2019
> anwar.m1 at gmail.com
> -----------------------
>
>
>
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