[gmx-users] Anisotropic pressure control

[Dallas B. Warren]

Why is it that what you have run with xy rigid and z couple not correct?  Fluctuating box volume is exactly what you would expect to get, and do get, with pressure coupling.

 

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

 

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Matteus Lindgren
Sent: Friday, 26 February 2010 8:24 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Anisotropic pressure control

 

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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