[gmx-users] Gromacs versions 4.0.5 and 4.5.4

[Sapna Sarupria]

Dear Itamar,

Thank you for your response. Why did you prefer to stick to 4.0.7? Is there
something particularly difficult to transfer from 4.0.7 version to 4.5
version?

Sapna

On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass <itamar.kass at monash.edu> wrote:

> 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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