[gmx-users] Gromos54a7 electrostatics interactions ?

Sim gmx simgmx at gmail.com
Fri Sep 22 10:21:11 CEST 2017


I would like to do simulations of lipids bilayers with gromos54a7
parameters. To do so, I want to use the same mdp parameters as Poger et al.
(the authors).

In their papers, they write : "Nonbonded interactions were evaluated using
a twin-range cutoff scheme: interactions falling within the 0.8-nm
short-range cutoff were calculated every step, whereas interactions falling
within the 1.4-nm long-range cutoff were updated every 10 fs, together with
the pair list. A reaction-field correction was applied to account for the
truncation of the electrostatic interactions beyond the long-range cutoff
using a relative dielectric permittivity constant of 62, as appropriate for
SPC water"

>From this, I conclude that my mdp file should contain something like (among
other parameters):

vdw-type = cut-off
rlist = 0.8
nstlist = 5
rvdw = 1.4
coulombtype = reaction-field
epsilon-rf = 62

My questions are:

1) Does "relative dielectric permittivity constant" indeed mean
"epsilon-rf" here (not epsilon-r) ?

2) What about the coulomb cut-off (rcoulomb) ? I think that in gromos53a6,
rcoulomb is often set to 0.9 (here I guess it would be 0.8 to match the
rlist). However, if the reaction-field correction is applied "to account
for the truncation of the electrostatic interactions beyond *the long-range
cutoff*", I would set rcoulomb to 1.4. As no explicit reference to rcoulomb
is done in the papers, I fear to miss something here.

3) If rcoulomb has indeed to be set to 1.4 as rvdw, it becomes possible to
use a verlet cut-off scheme to benefit from GPU acceleration. However, when
verlet cut-off scheme is used, mdrun shifts the nstlist and rlist to higher
values. Isn't it likely to impact the simulation reliability in such cases ?

Thank you in advance for your replies!

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