On Mon, Jan 9, 2017 at 3:10 AM, colvin <colvin4367.gmail.com> wrote:
> My system consisting a receptor/protein and a peptide. The trajectories
> post-
> autoimage produced multiple jumps in the rmsd plot for the whole system
> (receptor+peptide) - plot1. I can see that my peptide is jumping around the
> protein (corresponds to the jump in the plot) when I viewed the
> post-autoimage trajectory in VMD.
>
> However, if only the peptide or receptor rmsd is plotted, there is no such
> jump as observed in the plot1. Without autoimage, the peptide wanders far
> from the receptor at certain timestep, when viewing it with the VMD
This makes sense if autoimage is not working well for your system. If
you are calculating the RMSD of a single molecule, imaging by molecule
has no effect. There is only an issue when you calculate the RMSD of
multiple molecules since they may be imaged differently (which causes
jumps).
An improvement was recently made to the 'autoimage' command in the
GitHub version of cpptraj: https://github.com/Amber-MD/cpptraj
You can use the 'anchor' mask to specify only a small number of atoms
that should remain near the center of your unit cell - this improves
the performance of 'autoimage' in tightly packed systems.
-Dan
>
> Pls advise. Thanks.
>
> *Plot1:*
>
>
>
>
>
> *rmsd_receptor:*
>
>
>
> *rmsd_peptide:*
>
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--
-------------------------
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 Jan 09 2017 - 07:00:03 PST
