[gmx-users] Dynamics only for cavity in molecule.

[Mark Abraham]

Hi,

I have no idea whether that will help. Even if it is better, I am
struggling to see that annealing and freeze groups is a useful model, even
with frozen solvent.

Mark

On Fri, 4 Aug 2017 21:40 <nikolaev at spbau.ru> wrote:

> Well, that means that I need to use the group scheme?
> Or I can just add solvent and run the same thing?
>
> > Hi,
> >
> > I imagine nobody has ever tried with Verlet plus freeze plus annealing,
> so
> > it could be broken somehow... But frozen atoms around a cavity and no
> > electric field from solvent sounds like a model highly unlikely to be
> > related to reality...
> >
> > Mark
> >
> > On Fri, 4 Aug 2017 18:55 <nikolaev at spbau.ru> wrote:
> >
> >> Hello!
> >>
> >> I want to run dynamics only for a relatively small cavity of my
> >> molecule,
> >> with all other atoms frozen. For this reason, I also don't use solvent,
> >> because it won't move anyway. I run the simulation on GPU (gromacs
> >> 5.1.2),
> >> i.e. I use the Verlet scheme, pbc = xyz. However, when I start running
> >> simulations, I get violent behavior: the molecule immediately falls
> >> apart!! I am sure that I just made a silly thing in the parameters, but
> >> what is it? Here I attach my dynamics .mdp parameters:
> >>
> >>
> >> define = -DPOSRES
> >> integrator = md
> >> dt = 0.001
> >> nsteps = 1200000
> >>
> >> nstxout = 1000
> >> nstvout = 1000
> >> nstxtcout = 1000
> >> nstlog = 100
> >> nstenergy = 1000
> >>
> >> continuation   = no
> >> constraints    = none
> >>
> >> tcoupl = V-rescale
> >> tc_grps = System
> >> tau_t = 0.1
> >> ref_t = 0
> >>
> >> cutoff-scheme = Verlet
> >> ns_type       = grid
> >> nstlist       = 10
> >> rcoulomb      = 0.9
> >> rvdw          = 0.9
> >>
> >> coulombtype   = PME
> >> pme_order     = 4
> >> fourierspacing = 0.16
> >>
> >> pbc          = xyz
> >> gen_vel      = no
> >>
> >> DispCorr     = EnerPres
> >>
> >> ;
> >> ; Freezing atoms # this is all the atoms except for the cavity inside
> >> ;
> >> freezegrps = GroupDyna
> >> freezedim = Y Y Y
> >> ;
> >> ; Heating
> >> ;
> >> annealing = single
> >> annealing_npoints = 2
> >> annealing_time = 0 50
> >> annealing_temp = 0 298
> >>
> >>
> >> Thank you in advance,
> >> Dmitrii.
> >>
> >>
> >> --
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