[gmx-users] Gromacs versions 4.0.5 and 4.5.4

[Sapna Sarupria]

Dear All,

I have a simulation set up for a mixture of carbon dioxide and water system
which runs perfectly on Gromacs 4.0.5 version. I have run these simulations
at different temperatures and pressures, from the same starting
configuration and the simulation proceeds smoothly in the 4.0.5 version.
However, when I use exactly the same files to run the simulation in 4.5.4
version, the system crashes and writes out several pdb files. I was
wondering if there is anything specific that has been changed between the
two versions. I have pasted the mdp file of the simulations below. Any input
will be much appreciated.

MDP File

title               =  100% occupancy CO2 hydrate ; a string
cpp               =  /lib/cpp                 ; c-preprocessor
dt                  =  0.002                    ; time step
nsteps          =  15000000                 ; number of steps
nstcomm      =  10                       ; reset c.o.m. motion
nstxout          =  0000                    ; write coords
nstvout          =  0000                    ; write velocities
nstlog             =  25000                    ; print to logfile
nstenergy       =  500                      ; print energies
xtc_grps          =  OW_HW1_HW2_CO2
nstxtcout         =  1000
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                  = 270
tc-grps              =  System
tau_t                 =  0.5
Pcoupl             =  Parrinello-Rahman
Pcoupltype      =  semiisotropic            ; pressure geometry
tau_p                =  1.0   1.0                ; p-coupoling 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             =  260                      ; initial temperature
gen_seed             =  372340                   ; random seed
constraint_algorithm = shake
constraints         =  all-bonds

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Thank you,

Sincerely,
Sapna
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