Re: how do I restart umbrella sampling calculations?

From: Vermaas, Joshua (
Date: Tue Jan 24 2017 - 14:57:36 CST

Hi Olga,

Is this replica exchange or conventional umbrella sampling? For replica exchange, the script that sets up the run also automatically handles generating restart files. For convention umbrella sampling where the potential doesn't change with time, you don't need to do anything special. So long as you change the value for outputname, so that your dcd isn't overwritten, you will also get a new colvars.traj file that you'd concatenate to the old one and get the data you need for post-processing the particular window that crashed. Since the applied bias isn't time dependent, you restart it exactly as you started it the first time.


On 01/24/2017 01:45 PM, Olya Kravchenko wrote:
Hi all,

I have to restart my umbrella sampling calculations that quit due to hardware failure. What are the restart keywords for the colvars to use in the configuration file? I found one for ABF (colvarsInput <inputname>.restart.colvars.stat), but I don't see anything in tutorials or on this list about restarting US. Will the same option work for umbrella sampling? Is there anything else to change in the restart files so that colvar gets updated?

Does anyone have a sample restart file for US? (or ABF! I would appreciate that too for future reference.)

Thanks in advance!


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