Re: Metadynamics in NAMD

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Mon Apr 20 2009 - 12:21:46 CDT

Hello Wen, metadynamics is one of the methods provided by the
collective variables module, so you might want to look at that section
of the users' guide for 2.7b1. As of now, there isn't yet a tutorial
providing a summary of the (relatively long) documentation associated.
 You can take inspiration from the following, minimal configuration
for a distance between two atoms:

colvar {

    name d

    lowerBoundary 0.0
    upperBoundary 10.0
    width 0.5

    distance {
        group1 { atomNumbers 1 }
        group1 { atomNumbers 2 }
    }
}

metadynamics {
    colvars d
    hillWeight 0.01
    dumpFreeEnergyFile yes
}

---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
 phone: (+1)-215-573-4773
 fax: (+1)-215-573-6233
 mobile: (+1)-267-324-7676
 mail: giacomo.fiorin_<at>_gmail.com
 web: http://www.cmm.upenn.edu/
---- ----

On Mon, Apr 20, 2009 at 6:50 AM, $B<~J8>;(B <wenchangyu2006_at_gmail.com> wrote:
> Dear all,
> I know metadynamics is already implemented in the new release version of
> NAMD. But I can not find any instructions in user guide. Can anybody kindly
> provide a configuration file or a tutorial for metadynamics using NAMD?
> Thank you very much for any suggestions.
>
> Best,
> Wenchang

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