----- Original Message ----- From: Ting Zhou <[email protected]> Date: Tuesday, June 8, 2010 19:26 Subject: Re: [gmx-users] add external force To: Discussion list for GROMACS users <[email protected]>
> On 06/08/2010 11:18 AM, Mark Abraham wrote: > > > > > >----- Original Message ----- > >From: Ting Zhou <[email protected]> > >Date: Tuesday, June 8, 2010 19:13 > >Subject: [gmx-users] add external force > >To: [email protected] > > > > > 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. > > > >Mark > > > 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. Mark
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