Re: [AMBER] PROTEIN-DNA rmsd plot

From: David A Case <>
Date: Thu, 31 Dec 2020 21:47:41 -0500

On Thu, Dec 31, 2020, Syeda Amna Arshi wrote:

>rms first out rmsd.dat .CA
>and the resultant plot is attached below

See Dan's comments about your mask. Also, try to get in the habit of
reading the cpptraj output very carefully when something seems wrong.
I know it can be quite verbose, but lots of very helpful info is there, and
is the first place to study when problems arise.

But also check exactly how you are restarting each run -- as you note, the
drop in RMS seems to happen right at the beginning. Do a short restart,
exactly like you usually do, but just for 100 steps or so, with ntpr=1 and
ntwx=1. Compare the energies at the beginning of the restart with those
at the end of the previous run, to see if there is somediscrepancy you can
spot. Visualize what is happening on this short time scale. Basically,
you want to focus in on the part of the trajectory where the plots look

...good luck....dac

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Received on Thu Dec 31 2020 - 19:00:02 PST
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