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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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