[gmx-users] Dispersion correction for protein interfaces

Jason Grosch jgrosch at umail.iu.edu
Fri Mar 28 17:55:36 CET 2014


I'm planning on studying several large protein clusters using the gromos
54A7 force field with the following cutoff parameters: rlist=1.0 nm,
rcoulomb=1.0 nm (long range handled by PME), rvdw=1.4 nm, and the short
range list will be updated every 10 steps.  I am interested in studying
surface interactions, and I am uncertain if dispersion corrections is
appropriate to use.  From the gromacs 4.5.6 manual and from previous posts,
the dispersion correction is most appropriate for isotropic systems, and
can be inappropriate for large interfaces such as lipid membranes.  The
surface at proteins and protein clusters is anisotropic, does anybody know
if the dispersion correction should be used with proteins with a 1.4 nm
cutoff, as parameterized with gromos type force fields?  With such a
relatively large vdw cutoff does the dispersion corrections even matter?  I
don't see any differences when I use it, but I would like to be as correct
as possible. Was the gromos force fields parameterized using dispersion
corrections, I can't find a solid yes/no answer in the papers (I could have
missed it)?  I haven't had much luck finding answers to these in previous
posts, so any help or resources you can direct me to would be greatly

Thank You,
Jason Grosch

Theoretical Chemistry Group, Room C203G,
Center for Cell and Virus Theory
Department of Chemistry, Indiana University, Bloomington.
Email: jgrosch at indiana.edu

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