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

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, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: Hi all, I am facing a problem in constraining the crystallographic water molecules during invacuo simulat

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

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

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

Hi Anwar, The constraints are defined in spc.itp (or any of the other water models). So if you use -DPOSRES they are included automatically. Best, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of

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

Hi all, I am performing in vacuum simulation of a protein containing crystallographic water molecules. I want to constrain these water molecules, but pdb2gmx program doesnot generate the pr.itp for water molecules. How do I constrain these water molecules. regards Anwar --