[gmx-users] Using custom potential for electrostatics between protein and water

[Aram Davtyan]

Hello,

I am trying to use a custom electrostatic potential between protein and
water, with protein-protein and water-water potentials remaining the same.

I tried running the simulation with the following input script:

define                  = -DPOSRES   ; position restrain for protein
integrator              = md
dt                      = 0.002
nsteps                  = 10000 ; 2ns
nstlog                  = 1000
nstxout                 = 5000
nstvout                 = 5000
nstfout                 = 5000
nstcalcenergy           = 100
nstenergy               = 1000
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme-user
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
;
energygrps              = Protein Water Ion
energygrp-table         = Protein Water
;
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
;
ld_seed                 = 0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein Non-Protein
;
refcoord_scaling        = com

I have the following tables: `table6-12.xvg` and
`table6-12_Protein_Water.xvg` in the directory and run the simulation with
the following command lines

gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top -o
md_0_5.tpr
gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep table6-12.xvg

To test I set the electrostatic potential (f(r) and f'(r)) to zero in
`table6-12_Protein_Water.xvg` file. However, I find that the energies
calculated at the first step are identical to the case when custom
potentials are not used. What am I doing wrong?

Thank you in advance,

Aram