[gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

sapna sarupria sapna.sarupria at gmail.com
Tue Mar 30 17:47:01 CEST 2010

Hello all,

I have a simulation running for a hydrate (with CO2) and water in contact
with each other. I run the simulation at 280K at which the hydrate melts and
finally the system is just liquid water with CO2 in it. However, as the
simulation proceeds the box begins to expand in the z-direction and
decreases in the x-y direction considerably. Initially the box has
4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates
more) and is fine for another 10 ns but after that the dimensions in the x-y
direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this
point the simulation crashes since my cut-off distance are 1.2 nm.

I am using semi-isotropic pressure coupling but the pressure in the x-y
direction and z-direction are the same (=30.5 bar) and so is the
compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling
and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake
is used to maintain their geometry. The simulation time step is 2 fs. Can
someone tell me why such a thing happens? I have pasted my mdp file for
completeness. I am using Gromacs  4.0.5 and I run the simulations in
parallel using 4 processors. Values related to domain decomposition etc are
unchanged and the default values are used.

Any insights will be helpful. Thanks for the help.

MDP File:
title               =  CO2 hydrate + water      ; a string
cpp                 =  /lib/cpp                 ; c-preprocessor
dt                  =  0.002                    ; time step
nsteps           =  25000000            ; number of steps
nstcomm       =  10                           ; reset c.o.m. motion
nstxout          =  20000                    ; write coords
nstvout          =  20000                    ; write velocities
nstlog            =  25000                    ; print to logfile
nstenergy      =  500                   ; print energies
xtc_grps        =  OW_HW1_HW2_CO2
nstxtcout       =  500
nstlist             =  10                       ; update pairlist
ns_type          =  grid                     ; pairlist method
coulombtype   =  PME
rvdw                =  1.2                      ; cut-off for vdw
rcoulomb         =  1.2                      ; cut-off for coulomb
rlist                  =  1.2                      ; cut-off for coulomb
DispCorr          =  EnerPres
Tcoupl              =  Nose-Hoover
ref_t                 =  300
tc-grps             =  System
tau_t                 =  0.5
Pcoupl              =  Parrinello-Rahman
Pcoupltype       =  semiisotropic            ; pressure geometry
tau_p               =  1.0   1.0                ; p-coupling time
compressibility     =  4.5e-5  4.5e-5           ; compressibility
ref_p               =  30.5  30.5               ; ref pressure
gen_vel             =  yes                      ; generate initial vel
gen_temp            =  200                      ; initial temperature
gen_seed            =  372340                   ; random seed
constraint_algorithm = shake
constraints         =  all-bonds

Thanks a lot
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