Re: [AMBER] Discrepancy between mdcrd and output files for MD run

From: Carlos Simmerling <>
Date: Sun, 17 Jul 2016 17:08:21 -0400

The timing of output and mdcrd are not exactly synchronized, so they will
not exactly match. Details have been discussed before, search the archives
if you need more information.

On Jul 17, 2016 4:21 PM, "jandre17" <> wrote:

> Hello,
> I'm encountering an issues with a molecular dynamics run. The simulation
> runs smoothly, but the files of interest are the .out file and the .mdcrd
> file. I take a number of snapshots during the MD run for energies, etc.
> (recorded in the .out file) and afterwards I've created restart files for
> each snapshot using:
> trajin file.mdcrd 1 1000 1
> trajout file.rst restart multi
> My issue comes when I calculate the parameters for these restart files.
> I've taken the restart files and perform a zero-step MD run, as well as
> one-step minimizations, but the outputs do not match those from the
> original MD .out file, as I expected them to. EPtot, EELEC, and BOND differ
> by up to 50. Is there any suggestions as to where to look for errors?
> James
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Received on Sun Jul 17 2016 - 14:30:03 PDT
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