[gmx-users] Imaging in PBC simulations -summary

Martin LEPSIK martin.lepsik at ibs.fr
Tue Apr 25 10:45:59 CEST 2006

Dear Jochen and Tamas,
thanks for your replies. I tried both, the "trjconv -fit" postprocessing 
and setting "comm_mode" for mdrun and actually only the latter worked 
fine. In the former, protein drifts toward the box side and jumps out 
for some frames, leaving its bound ions inside the box. Better to remove 
translation during the run.

All the best,


>> Dear GROMACS users,
>> I would like to ask you maybe a trivial question: What is the best 
>> way to image a protein with a ligand inside
>> a triclinic water box?
>> I run an MD in GMX-3.3 with nstcomm=1, "comm_grps" and not set. I 
>> watch the movie in VMD,
>> loading first a starting gro and than the trr. The problem is that 
>> the protein creeps out of the box (the same happens
>> when using ngmx).
>> I have tried various variants of post-processing using trjconv -fit 
>> (translation) -pbc (inbox, whole) -center (tric),
>> groups for fitting: protein or system. But in any case, the result is 
>> the same.
>> Could you please advice me how to solve this? Whether it is better to 
>> include some parameter for
>> mdrun or to post-process in a different way?
>> Looking forward to hearing from you.
>> Yours sincerely,
>> Martin Lepsik
> You can either
> use comm_grps = Protein and comm_mode = Linear
> or
> use trjconv with the -fit option and fit your protein on the starting 
> position after finishing the simulation.
> Cheers, Jochen

Martin Lepsik, Ph.D. 
Laboratoire de Dynamique Moléculaire (LDM)
Institut de Biologie Structurale
41, rue Jules Horowitz
38027 Grenoble Cedex 1, France
tel: +33-4-3878-4780
e-mail: martin.lepsik at ibs.fr

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