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

[Mark Abraham]

Hi,

You've described the feature correctly. Whether it is useful in a study
design is another matter :-)

Mark

On Sun, Nov 19, 2017 at 8:00 PM Aram Davtyan <davtyan.aram at gmail.com> wrote:

> 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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