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 [email protected] +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of Matteus Lindgren Sent: Friday, 26 February 2010 8:24 PM To: [email protected] 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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