[gmx-users] jump problem

[Tsjerk Wassenaar]

Hey :)

Cluster the first frame and write out as new reference structure. Then run
with that reference, removing jumps.

Cheers,

Tsjerk
On Mar 18, 2015 12:46 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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