[gmx-users] How to apply trjconv -nojump to a part of a system

Justin Lemkul jalemkul at vt.edu
Wed Jul 10 12:48:42 CEST 2013

On 7/9/13 7:13 PM, Bin Liu wrote:
> Hi All,
> For the convenience of visualization, I need to remove the jump of one
> component (say a protein) of the system at the boundary. I don't need to,
> or say I need not to remove the jump of the other components (say a lipid
> bilayer), since otherwise the system will look falling apart. I noticed I
> can cluster a part of a system, then output all the atoms in the system in
> which only the part is clustered, and the other components unchanged. Does
> GROMACS have similar function when *-nojump* is used?
> If this can not be accomplished directly, is there a way to circumvent it?
> I figured out a way, but haven't implemented it. I can plug the coordinates
> of the protein treated with *-nojump* into the trajectory of the whole
> system which is not treated with *-nojump*. It is kind of substituting the
> coordinates of one component in one trajectory with the coordinates of the
> same component in another trajectory. Is there anyone aware of a tool or a
> script to do this job?

Would this actually work?  I would think the protein would collide with other 
elements of the system - solvent, etc.  Wouldn't fitting be a better option 
here?  If the protein moves in relation to a surface, something like trjconv 
-fit transxy is probably quite useful.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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