Hi all, I've encountered a problem while trying to run Gromacs on my coarse-grained molecule. I've already performed the initial energy minimization. I tried to run the inital MD simulation, but the job was cut short due to a segmentation fault, as mentioned in the output file:
^Mstep 0^Mstep 100, will finish Wed Dec 16 16:55:17 2009^Mstep 200, will finish Wed Dec 16 07:04:11 2009^Mstep 300, will finish Wed Dec 16 12:59:33 2009^Mstep 400, will finish Wed Dec 16 09:02:03 2009^Mstep 500, will finish Wed Dec 16 12:12:01 2009^Mstep 600, will finish Wed Dec 16 14:18:47 2009^Mstep 700, will finish Wed Dec 16 15:49:22 2009^Mstep 800, will finish Wed Dec 16 13:29:16 2009^Mstep 900, will finish Wed Dec 16 14:45:15 2009^Mstep 1000, will finish Wed Dec 16 15:46:03 2009 /opt/gridengine/default/spool/ compute-0-7/job_scripts/182710: line 28: 18851 Segmentation fault (core dumped) $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr /opt/gridengine/default/spool/compute-0-7/job_scripts/182710: line 31: -s: command not found Does anyone know what could be causing the problem? Should it be of interest, my em.mdp is included at the bottom. Thanks for your help! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ em.mdp ; VARIOUS PREPROCESSING OPTIONS = title = cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit = 0 dt = 0.02 nsteps = 1000 ; ENERGY MINIMIZATION OPTIONS = ;emtol = 0.00001 ;emstep = 0.1 ;nstcgsteep = 1000 emtol = 10 emstep = 0.01 nstcgsteep = 1000 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ md.mdp ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = md ; start time and timestep in ps tinit = 0 dt = 0.020 ;nsteps = 10000 ; initial step nsteps = 10000000 ; 200 ns @ dt=0.02 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps =
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