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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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

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

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