[gmx-users] Calculating electric field vector at snapshots
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jun 5 08:53:32 CEST 2008
Aaron Fafarman wrote:
> Dear GMX community,
> I would like to calculate the electric field vector at a point in
> space in a protein at many snapshots during an MD trajectory. I
> haven't found a built-in function for doing this in Gromacs--is there
> one? If not, would people please comment on this proposal for how to
> do this:
> 1. Include a virtual site referenced to the two atoms (constructing
> particles) that define the point in space I would like to interrogate.
> Give it only a very small charge, so small that the force from the
> virtual site to the constructing particles is negligible.
> 2. Have the calculation output the force on the virtual site at a
> determined interval by setting nstfout in the.mdp file
> 3. Divide the force by the small charge, and hence get the field
> It seems like this should work as long as the force on virtual sites
> is reported in the output of forces from nstfout, and as long as using
> such a small charge on the virtual site will not run into rounding
> errors. Also I'm presuming that the coulomb interaction is not
> calculated between the constructing atoms and the virtual site--is
> that correct? Any thoughts?
I think it will work. Just try it.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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