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

[Mark Abraham]

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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