[gmx-developers] External Electric Field

Grzegorz Nawrocki aksonik at gmail.com
Tue Nov 29 14:23:08 CET 2011

I'm writting to you because I have a problem with modifying Gromacs code. I
wonder if you ever have found similar problem. I will be very grateful for
any advice or information about people who did the same things before:

I do simulations of proteins on solid surface. I modified force field in a
way, that atoms of solid surface have charges equal zero. Values of
potential and force comming from real charges on these atoms I determined
in junctions of 3D lattice over surface and located in separated file. I
modified Gromacs code to read this file and use calculated values in
simulations. During simulations potential and force for atoms located
between junctions are determined as weighted mean of neighbouring junctions.

And all this look good, but my simulations crash, because of Lennard-Jones
interactions. I found that many angstroms over surface LJ energy is
extremely big. What is more, it is different in the same place but over
other unit cells of surface. I didn't change parts of code that are
connected with LJ calculations.

I know, it is difficult to say something on the basis of such description,
but maybe you have some ideas what I overlooked, that may gives such

Best wishes,
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20111129/dce53389/attachment.html>

More information about the gromacs.org_gmx-developers mailing list