Dear experts,
I am trying to run MD on a protein in water above a flat surface of TiO2 in
a cubic box with pressure control. All the atoms of TiO2 are frozen and I
therefore think that anisotropic pressure control must be used. I tried
allowing box fluctuations in the direction of the normal vector (the z-axis)
of the TiO2 surface but the box volume then oscillates during the whole
simulation. The same parameters worked for a simulation of protein+water
without the frozen TiO2 surface.
How can I use pressure control for a system with a frozen surface that
extends through the whole box? Ive read the posts about membrane simulations
but membranes are flexible so I think those suggestions might not apply.
The important part of the input file was as follows:
nstlist = 10
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 1.2
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.2
epsilon-r = 1
epsilon_rf = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.4
DispCorr = EnerPres
table-extension = 1.5
energygrp_table =
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
optimize_fft = yes
Tcoupl = Nose-hoover
tc-grps = protres RUT solcl
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
Pcoupl = Parrinello-Rahman
Pcoupltype = anisotropic
tau_p = 2.0 2.0 2.0 2.0 2.0 2.0
compressibility = 0.0 0.0 5e-5 0.0 0.0 0.0
ref_p = 0 0 1.01325 0 0 0
gen_vel = yes
gen_temp = 310
gen_seed = 1993
constraints = hbonds
constraint-algorithm = lincs
continuation = yes
lincs-order = 4
lincs-iter = 4
freezegrps = frozen
freezedim = Y Y Y
Thanks
Matteus
---------------------------------------------------------
Matteus Lindgren, graduate student
Department of Chemistry, Umeå University
SE-901 87 Umeå, Sweden
Phone: +46 (0)90-7865368
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