[gmx-users] Pressure Coupling Problem

[chris.neale at utoronto.ca]

Hi Ilya,

First thing that comes to mind is that it is strange to couple a  
coulombic switching function with PME. While this could possibly be  
done correctly, I doubt that it is in fact done in the way that you  
expect (i.e. correctly) in gromacs. In fact, I think that grompp/mdrun  
should probably throw an error here -- unless it is actually handled  
in the proper way, and a developer could help you here to figure out  
if you are indeed getting what you desire.

coulombtype              = PME
rcoulomb-switch          = .9
rcoulomb                 = 1.0

However, it is not clear to me that this should cause a system to  
"continuously expand".

Still, you do not give very good information about what you mean by  
"continuously expand". Can you please provide some information on  
that? e.g. amount of time and total volume change.

Chris

-- original message --

Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
run NVE it conserves energy with appropriate parameter settings. If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the system just continuously expands. My parameters are as follows.
Any ideas?

Best,

Ilya

;
;       File 'mdout.mdp' was generated
;       By user: relly (508)
;       On host: master.simprota.com
;       At date: Fri Mar  6 20:17:33 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include                  =
; e.g.: -DI_Want_Cookies -DMe_Too
define                   =

; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.004
;nsteps                   = 250000
nsteps                   = 2500000
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part          = 1
init_step                = 0
; mode for center of mass motion removal
comm_mode                = linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm_grps                = system

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0

; Output frequency for energies to log file and energy file
nstlog                   = 10
nstenergy                = 10
; Output frequency and precision for xtc file
nstxtcout                = 250
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps                 = protein
; Selection of energy groups
energygrps               =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 5
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic_molecules       = no
; nblist cut-off
rlist                    = 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = PME
rcoulomb-switch          = .9
rcoulomb                 = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r                = 80
epsilon_rf               = 1
; Method for doing Van der Waals
vdw-type                 = Switch
; cut-off lengths
rvdw-switch              = .9
rvdw                     = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Seperate tables between energy group pairs
energygrp_table          =
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1.e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = V-rescale
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1
ref_t                    = 298.0
; Pressure coupling
Pcoupl                   = Berendsen
Pcoupltype               = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 10
compressibility          = 4.5e-5
ref_p                    = 1.01325
; Scaling of reference coordinates, No, All or COM
refcoord_scaling         = No
; Random seed for Andersen thermostat
andersen_seed            = 815131
-------------- next part --------------
An HTML attachment was scrubbed...