[gmx-users] add external force
mark.abraham at anu.edu.au
Tue Jun 8 16:07:07 CEST 2010
----- Original Message -----
From: Ting Zhou <coomteng at gmail.com>
Date: Tuesday, June 8, 2010 19:26
Subject: Re: [gmx-users] add external force
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> On 06/08/2010 11:18 AM, Mark Abraham wrote:
> >----- Original Message -----
> >From: Ting Zhou <coomteng at gmail.com>
> >Date: Tuesday, June 8, 2010 19:13
> >Subject: [gmx-users] add external force
> >To: gmx-users at gromacs.org
> > > Hi,
> > >
> > > I would like to add an external force f(x) on some atoms during
> > > the simulation, where x is the Cartesian coordinates of
> these atoms.
> > >
> > > Each component of the force can only be calculated with the
> > > whole set of coordinates, i.e., (f1, f2, ..., fn) = f(x1, x2,
> > > ..., xn)
> >If you potentially need to know every coordinate to calculate each
> >force, then you will have to either run in serial, or emulate the
> >behaviour in write_trxframe to gather the coordinates and
> scatter the
> >forces at useful time.
> Are you talking about modifying the source?
Yes. Perhaps TINKER or something is more amenable to the kind of "computational experiment" that it sounds like you might be doing.
> Is there a lagged
> script interface to calculate forces?
I don't know what this is, but no.
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