Re: restart glitch - return to original structure

From: Josh Vermaas (
Date: Fri Apr 15 2022 - 16:00:16 CDT

Hi Dan,

Could you post your NAMD configuration file? My first thought is that
you might be mixing up a .restart.coor with a .coor file. The
.restart.coor files are written every restartfreq steps, while the .coor
files are only written at the very end of a simulation.


On 4/15/22 2:04 PM, Strahs, Dr. Daniel Bernard wrote:
> Hello all:
> I'm recently experiencing a weird glitch, and I'm looking for some
> ideas to throw at it.
> I'm currently using an older NAMD: 2.7. Sometimes, when the system
> restarts a run (either at the conclusion of a 1-ns segment, or restart
> after a fatal error), the simulation will restart at an earlier structure.
> I've checked the outputs: correct filenames are being used. I've tried
> to diagnose by using VMD to export the final snapshot of a trajectory
> and comparing those exported coordinates to the final coordinate file
> completed at the end of a 1-ns segment: the files match. So the
> structures being used in these erroneous simulations are not coming
> from the exported coordinates.
> Is it possible that the restart files are being altered to an earlier
> state? The computer system has 12 nodes, 4 cpus/node: could a
> malfunctioning node cause this problem? Any thoughts/insights would be
> very welcome.
> Thanks in advance!
> Dan Strahs
> Pace University

Josh Vermaas
Assistant Professor
MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology
Michigan State University;!!DZ3fjg!rtvQ76oWvDMx-MIwdo0-GRUvMwIe5_vY881G6AXMOPmj7qU_nI--xabaBl7PIGa0TA$ 

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