[gmx-users] (no subject)

[Tsjerk Wassenaar]

Hi Anjelika,

The version of mdrun_mpi you're using is an older version of Gromacs
(than used for setting up the simulation), not capable of reading the
newer .tpr files. Be sure to use 3.3.3 also for the production run.

Cheers,

Tsjerk

On Thu, Aug 28, 2008 at 7:47 PM, Anjelika Gasilina
<s10.agasilina at wittenberg.edu> wrote:
> Greetings!
>
> I am trying to perform free energy calculations on my protein system. I am using Gromacs 3.3.3 double precision for Linux.
> The grompp runs fine and the .tpr file is created, but as soon as I submit the batch job, it dies and I receive the following error message
>
> Back Off! I just backed up em5.log to ./#em5.log.1#
> Getting Loaded...
> Reading file em.tpr, VERSION 3.3.3 (double precision)
> Fatal error: reading tpx file (em.tpr) version 40 with version 31 program
> mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 10.1.1.7, rank 0, killing all.
>
> I am not sure what the warning message is saying since I have no idea what it is referring to.
>
> Currently I am still stuck on energy minimization. Here is my em.mdp file
>
> RUN CONTROL PARAMETERS =
> integrator               = steep
> nsteps                   = 20000
> ; Output frequency for energies to log file and energy file =
> nstlog                   = 1
> nstenergy                = 1
> ; ENERGY MINIMIZATION OPTIONS =
> ; Force tolerance and initial step-size =
> emtol                    = 100
> emstep                   = 0.01
> ; Max number of iterations in relax_shells =
> niter                    = 20
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist                  = 1
> ; ns algorithm (simple or grid) =
> ns_type                  = grid
> ; Periodic boundary conditions: xyz or none =
> pbc                      = xyz
> ; nblist cut-off         =
> rlist                    = 1.0
> domain-decomposition     = no
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; Method for doing electrostatics =
> coulombtype              = pme
> ;rcoulomb-switch          = 0
> rcoulomb                 = 1.0
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon-r                = 1
> ; Method for doing Van der Waals =
> vdw-type                 = switch
> ; cut-off lengths        =
> rvdw-switch              = 0.8
> rvdw                          = 1.0
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid =
> fourierspacing           = 0.1
> ; 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                = 6
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
> optimize_fft             = no
> ; Free energy control stuff
> free_energy              = yes
> init_lambda              = 0.6
> delta_lambda             = 0
> sc_alpha                 =0.5
> sc-power                 =1.0
> sc-sigma                 = 0.3
>
> Thank you all,
>
> Anjelika
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623