Re: restart glitch - return to original structure

From: Strahs, Dr. Daniel Bernard (
Date: Fri Apr 15 2022 - 16:07:48 CDT

Hi Josh:

Thanks for that idea; I think it's unlikely, as I do have some years of experience. I've attached input configuration files from two adjacent segments.

Take care and thanks again!

Dan Strahs

Pace University

From: Josh Vermaas <>
Sent: Friday, April 15, 2022 5:00 PM
To:; Strahs, Dr. Daniel Bernard
Subject: Re: namd-l: restart glitch - return to original structure

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!uJcwrINjy7HlWOI4uS_sFwC7zSDVwOmK3xf1JF4f0EP2EoalL3J5OTz9urJovtG26g$ <*3A*2F**2F&data=05*7C01*7C*7Cdc4da9994f01438b421808da1f22f2f8*7C0799c53eca9a49e88901064a6412a41d*7C0*7C0*7C637856532649856541*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=xgj1UUs0ocU3oixaFG3*2B6YVHA0GN8p0I*2BXvOXwUmJWU*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!DZ3fjg!uJcwrINjy7HlWOI4uS_sFwC7zSDVwOmK3xf1JF4f0EP2EoalL3J5OTz9urLkjWtBVw$ >

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