Re: Continuing metadynamics run

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri May 04 2018 - 10:59:30 CDT

Are correctly restarting the simulation?
http://www.ks.uiuc.edu/Research/namd/2.12/ug/node12.html#SECTION00062100000000000000
http://colvars.github.io/colvars-refman-namd/colvars-
refman-namd.html#sec:colvars_input

Giacomo

On Fri, May 4, 2018 at 11:25 AM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> 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
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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