Re: Continuing metadynamics run

From: Giacomo Fiorin (
Date: Fri May 04 2018 - 10:59:30 CDT

Are correctly restarting the simulation?


On Fri, May 4, 2018 at 11:25 AM, Rabeta Yeasmin <>

> Hi NAMD users,
> I am running metadynamics in NAMD to find the binding interface between
> two proteins. I set up the colvar as distance between the two protein and
> rotate one of the protein around another. As I can not finish the whole
> simulation in one run, I continue run one after another. But I have found
> that it actually assume each run as one cycle means it try to explore all
> the colvar variable in one run and assume each run as different rather than
> continuing from the last run. Like in one run (5ns), the distance the two
> protein distance varies from 20 to 12 and rotation may be 90 degree. In
> next run I want it to continue explore from 12 to 0 and rotate 90 to 360,
> but in next run it still explore 20 to 12 or 8. I am wondering what can I
> do to continue the run.
> Thanks.
> Rabeta Yeasmin

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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