[gmx-developers] External E Field PME

Timothy DeWolf tdewolf at uvic.ca
Sat Dec 13 09:50:27 CET 2014


  I just signed up for this list, and I'd like to contribute to GROMACS.
I'm a Ph.D. student, with relevant background in physics, biochemistry, and

  I'm interested in extending GROMACS' abilities to impose user-defined
electric fields, and specifically interested in spatially constant
time-varying fields.  I looked at calc_f_el in sim_util.cpp, having read
"Patching mdrun" on the GROMACS website, and see that it would be fairly
easy to modify.  But I'm concerned about this "WARNING" in the comment lines
above the function definition, which state that there "can be problems with
the virial."

  The solution proposed there is to implement the "externally imposed" field
directly in PME.  I'm not an expert yet, but I read the relevant section in
Berendsen's book and the '95 smooth PME paper to get up to speed; I haven't
yet got to a detailed study of pme.c.

  What is the best place to begin?  I suppose that a linearly increasing
potential mapped to each charge along with the FT lattice sum terms in the
PME routine(s) would do it?  May I please ask for any suggestions, ideas or
hints (possibly including relevant spots in the code)?




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