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

[nikolaev at spbau.ru]

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.