Hi,
Instead of image/center, try ‘autoimage’.
-Dan
On Sat, Apr 21, 2018 at 2:36 AM <g.bakrani.sci.ui.ac.ir> wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Sat Apr 21 2018 - 10:00:01 PDT
