[gmx-users] jump problem

[Justin Lemkul]

On 3/17/15 9:03 PM, Ahmet yıldırım wrote:
> Dear users,
>
> I tried to remove the jumps of a structure after simulation but I couldn't
> do it. The structure is heterodimer. I tried the following ways:
>
> 1)
> -gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump
> -gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -pbc mol -ur
> compact -center
>
> 2)
>   gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -center
>
> 3)
> -gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -center
> -gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -fit rot+trans
>
> Do you have any suggestion(s)?
>

Fitting to any default group is unlikely to work in multimeric systems.  Use a 
custom index group to center on one subunit or some selected subset of atoms in 
one protein (e.g. some interfacial residues, or something convenient).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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