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? Thanks, -Aaron _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
