[gmx-users] wandering

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Thu Jul 10 10:12:01 CEST 2003

David wrote:
> On Wed, 2003-07-09 at 23:37, Nagy, Peter I. wrote:
>>Dear Gromacs Users!
>>    I think, this problem has emerged many times, so please direct me
>>if there are answers somewhere.
>>    I performed a 10 ps test run for a protein consisting of 26
>>residues and about 600 water molecules. Everything went seemingly
>>properly. When I looked at the protein dynamics using ngmx I found
>>that the protein was much out of the box. I assume that a
>>translational motion was allowed although the center of mass should
>>not move, and originally the software places the protein within the
>>box, I presume. There must be periodic boundary conditions, so the
>>protein would remain solvated even leaving the box, yet I am worried
>>about the translation.
>>    The question is: how could I keep the solute strictly within the
>>box, thus
>>preventing translation?
> you can define center of mass motion removal group (com_groups IIRC)
> but do you really want to stop the protein from diffusing?
> You won't be able to calculate the diffusion constant!
I think he is just confused, because the molecules are not cut while
diffusing through the box borders in pbc and hence seem to stick
out of the box.

This is a job for...
trjconv -center -pbc whole

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785

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