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

[Mark Abraham]

Hi,

In the group scheme you can turn on energy-group exclusions to get this
working, but of course all of those states are sampling unphysical things
from a broken forcefield. That can be OK, but you will have to be able to
defend that claim.

Mark

On Sun, Nov 19, 2017 at 6:49 AM Aram Davtyan <davtyan.aram at gmail.com> wrote:

> 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
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