[gmx-users] Calculating electric field vector at snapshots

Aaron Fafarman aarontf at stanford.edu
Thu Jun 5 03:01:18 CEST 2008

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?



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