[gmx-users] Turning off electrostatics between protein and water, then protein and protein
Mark Abraham
mark.j.abraham at gmail.com
Sun Nov 19 21:42:24 CET 2017
Hi,
Oh, I see. Yes that feature turns off both kinds of non-bonded
interactions. Then there is nothing useful for what you want.
Mark
On Sun, Nov 19, 2017 at 8:32 PM Aram Davtyan <davtyan.aram at gmail.com> wrote:
> 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
> > > > > --
> > > > > Gromacs Users mailing list
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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
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