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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
