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

[nikolaev at spbau.ru]

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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