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

[Aram Davtyan]

Hi Mark,

I apologize if I did not describe my problem correctly the first time, but
I need the VdW interactions to stay on between all atoms at all times. I
only need to turn off the electrostatic interactions between water and
proteins.

Thanks,

Aram

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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> End of gromacs.org_gmx-users Digest, Vol 163, Issue 69
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-- 
Aram Davtyan, Ph.D.
Center for Theoretical Biological Physics
Rice University
E-mail: adavtyan at rice.edu <adavtyan at uchicago.edu>
Phone: (919)265-8369