[gmx-users] Anisotropic pressure control

[Matteus Lindgren]

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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