[gmx-users] Gromacs versions 4.0.5 and 4.5.4

[Itamar Kass]

Hi Sapna,

I had the same problem few weeks ago.

Apparently, some parameters are different (eg. nstpcouple).

Cheers,
Itamar

PS I found out that I prefer to stick to 4.0.7.



On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote:

> 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 
> 
> -------
> 
> 
> Thank you,
> 
> Sincerely,
> Sapna
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-----
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
============================================

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