[gmx-users] Turning off electrostatics between protein and water, then protein and protein

[Aram Davtyan]

Hello,

I am running simulations of two protein domains in tip4p water and 0.15M
salt concentration that contain up to 650,000 atoms total. The protein
domains are separated from each other at the start of each simulation and I
am measuring how the distance between them changes over time.

Now, I need to do the same simulations, but with electrostatics between
proteins and water turned off (with water-water, protein-protein,
ion-water, ion-protein electrostatics remaining). Then I need to repeat
that, but additionally turning off electrostatics between the two domains.
Water-water, ion-water, ion-protein, intra-domain electrostatics should
remain on.

What will be the best way to do this?

I am using CHARMM27 force field and the following settings to run the
production simulations:

integrator              = md
dt                      = 0.002
nsteps                  = 1000000 ; 2ns
nstlog                  = 1000
nstxout                 = 5000
nstvout                 = 5000
nstfout                 = 5000
nstcalcenergy           = 100
nstenergy               = 1000
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
;
tcoupl                  = Nose-Hoover
tc_grps                 = Protein Non-Protein
tau_t                   = 1.0     1.0
ref_t                   = 300.0   300.0
;
pcoupl                  = Parrinello-Rahman
pcoupltype              = isotropic
tau_p                   = 5.0
compressibility         = 4.5e-5
ref_p                   = 1.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein Non-Protein
;
refcoord_scaling        = com


I have tried to use the energy groups (energygrp-table) to specify
interaction tables between water and protein, where I would set the
electrostatic potential to zero. However, given that energygrp-table and
Varlet cutoff-scheme are incompatible, I could not make it work. But it is
possible that I did something wrong.

Thank you in advance,

Aram