Hello dear amber users,
I have faced a problem with analysis of my simulations. The case is
a box with 7 34-residues peptides were placed in the octahedral box in
definite regular distances in X,Y and Z axis from each other in a 30Aº
spaced grid (one molecule in the center and others around it in
different axis).All steps were done by amber14,ambertools15 and ff14SB
force field. I want to analyze the association of these peptides but
in visualization part with VMD , the problem occurs; box jumping. 2
molecules go out from one side of the box and return to from other
side. It seems autoimage and center commands do not work here.
Parm X.prmtop
trajin X.mdcrd
center :1-238 mass origin
image origin center familiar
Also I tried all commands in the mailing list like:
*
image familiar com :1-238
*
[unwrap :1-238
center :1-238 mass origin
image origin center familiar]
But it didn't work. I hope you can help me with this.
Regards
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Received on Sat Apr 21 2018 - 00:00:02 PDT
