Re: [AMBER] production error.

From: David Case <>
Date: Tue, 14 Feb 2017 09:15:29 -0500

On Tue, Feb 14, 2017, Saman Yousuf ali wrote:

> then I added iwrap=1 flag and rerun siumlation using 26 rst file. When
> job finished, I reimaged mdcrd files using autoimage keyword and plotted
> rmsd as well. Upon loading reimaged trajectories into VMD, I observed
> that both subunitsdisplaced from their starting positon. After 8ns rmsd
> of dimer complex jumps from 5 to 25 angstroms.

Autoimage can sometime fail to find the desired "anchor" to which imaging
should be done, although it is in fact pretty smart. You may need to specify
the anchor molecules yourself, so that one monomer in the dimer doesn't get
imaged relative to the other. See the image commands in manual.

And, of course, visualize your trajectory to see exactly what is
happening--that often makes clear things that seem curious or confusing if
all you are looking at is an RMSD vs. time plot.


AMBER mailing list
Received on Tue Feb 14 2017 - 06:30:03 PST
Custom Search