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 Wed Apr 18 2018 - 22:00:02 PDT
