Re: Link between simulations

From: Suresh (
Date: Mon Apr 22 2013 - 01:37:00 CDT


There are many tools available to combine the trajectories.
tools like catdcd in vmd, carma, wordom tools which are simple and easy to use.
for more details, see the respective documentation and use it.

For restarting jobs, use the files coor, vel, xsc generated during simulations. Instead of coordinates and temperature in previous simulation, use the current coor, xsc, vel files and also change the firsttimestep to the current number of steps.
for more informations, read the namd manual.

hope this helps


----- Original Message -----
From: "Mihaela Drenscko" <>
Sent: Sunday, April 21, 2013 1:48:36 AM
Subject: namd-l: Link between simulations


I was running a simulation with 10 million steps for DMPC molecule. The job was killed by high performance computing because it took too much time. So I decided to divide the job in two parts, each with 5 million steps. Now, how do I link the second job with the first, so that in the end it will look like I have run the simulation with 10 million steps? How do I use restart files?

Thank you,


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