[AMBER] autoimage

From: colvin <colvin4367.gmail.com>
Date: Mon, 9 Jan 2017 16:10:57 +0800

Dear all,

I am having a problem with the trajectories imaging (pls see plot1 below).

My system consisting a receptor/protein and a peptide. The trajectories
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

Pls advise. Thanks.




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(image/png attachment: rmsd_peptide.png)

(image/png attachment: rmsd_receptor.png)

(image/png attachment: plot1_rmsd_all.png)

Received on Mon Jan 09 2017 - 00:30:02 PST
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