Hi,
If all 7 peptides are independent, there is likely no way to prevent
this "jumping" unless you use the 'unwrap' command on the coordinates.
However, keep in mind that almost every command in cpptraj uses the
minimum image convention for distances, so "unwrapping" would only be
for visualization purposes.
If the 7 peptides are in a complex and jumping is still occurring
after 'autoimage', please send me off-list a topology file and a few
trajectory frames that illustrate the problem you are having so I can
try to reproduce the issue.
-Dan
On Sun, Apr 22, 2018 at 3:49 PM, <g.bakrani.sci.ui.ac.ir> wrote:
> Dear Amber users,
>
> I intended to investigate peptide associations via MD simulation, so
> I put 7 peptides in a truncated octahedron box with 30A hydration
> layer. But, as I visualized my simulation in VMD, I realized that some
> of my peptides moved to the edge of the box and then jumped to the
> other side.
>
> Therefore, I have tested several commands in cpptraj such as _center
> with autoimage _and set all peptides in the atom mask in order to
> solve this problem. But again those peptides keep jumping from one
> side to the other.
>
> I would be so much appreciated if somebody could help me to tackle
> this problem.
>
> Here is my command used in cpptraj:
>
>
>
> 1.parm x.prmtop
>
> trajin prod.mdcrd
>
> autoimage fixed :1-238 origin familiar
>
> center
>
>
>
> 2.parm
>
> trajin
>
> center :1-238 mass origin
>
> image origin familiar
>
>
>
> 3.parm
>
> trajin
>
> image familiar com :1-238
>
> Best regards,
> _______________________________________________
> AMBER mailing list
> 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 Mon Apr 23 2018 - 07:00:06 PDT
