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

From: jandre17 <jandre17.masonlive.gmu.edu>
Date: Sun, 17 Jul 2016 20:21:31 +0000


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?

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Received on Sun Jul 17 2016 - 13:30:02 PDT
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