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

[Aram Davtyan]

Hi Mark,

I am not sure I understood. If I for example say "energygrp-excl = Protein
Water" would not I turn off all the non-bonded interactions between water
and protein? Or did you mean something else?

Thanks,

Aram


> 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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