[gmx-users] Turning off electrostatics between protein and water, then protein and protein
Mark Abraham
mark.j.abraham at gmail.com
Sun Nov 19 22:52:38 CET 2017
Hi,
You can't decompose the "turning off" in the FE code by groups. You can
turn off the coulomb in the protein, but that turns off its interactions
with itself, solvent, and anything else
Mark
On Sun, Nov 19, 2017 at 9:27 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/19/17 3:42 PM, Mark Abraham wrote:
> > Hi,
> >
> > Oh, I see. Yes that feature turns off both kinds of non-bonded
> > interactions. Then there is nothing useful for what you want.
>
> Couldn't this be done with the free energy code?
>
> Turn off protein-water electrostatics by running in the lambda=1 state
> with:
>
> couple-lambda0 = vdw-q
> couple-lambda1 = vdw
> couple-intramol = no
>
> Then switch to couple-intramol = yes to turn off protein-protein
> interactions.
>
> I imagine it would be a huge memory hog and would run really slowly, but
> it's a possible solution.
>
> -Justin
>
> > 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
> >>>>>> --
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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
> >> --
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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