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Author Topic: restarting a molecular dynamics calculation  (Read 2320 times)


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restarting a molecular dynamics calculation
« on: December 09, 2014, 11:55:44 AM »


I am doing a molecular dynamics calculation, but the calculation stop after 430 steps, apparently without a cause. I want to continue the calculation, but I do not find in the users manual any precise suggestion how to do it without loosing the previous calculated information.

National University of Mexico


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Re: restarting a molecular dynamics calculation
« Reply #1 on: December 18, 2014, 07:23:46 PM »

When you run an MD simulation, you should find two files in the scr directory: restart.md and restart.mdRND  These contain the restart information which is output by TeraChem.  If you then submit a job with the keyword:

restartmd /path/to/restart.md

the calculation will be restarted from where it left off (Note that BOTH the restart.md and restart.mdRND files are needed; if you wish to rename or copy these to save them for future use, please make sure that the names are x and xRND, i.e. restart1.md and restart1.mdRND).  Please note that the number of MD steps (nstep) is interpreted as the total desired length of the simulation (including the steps already taken and recorded in the restart.md file).  Also note that you can control the frequency with which TeraChem records steps in restart.md by setting the restartmdfreq keyword, e.g.

restartmdfreq 10

will store the MD information every 10 time steps.  The default is to save the information every 100 time steps.