*Dear all,* *I am trying to simulate a system of drug carrier consisting of HSPC/CHOL in the form of a vesicle. The code works well for the system when the CHOL molecules are not inserted. As I include CHOL molecules I face this error:*
*starting mdrun 'Chol/HSPC VESICLE'900000 steps, 27000.0 ps.step 0[compute-0-3:30916] *** Process received signal ***[compute-0-3:30916] Signal: Segmentation fault (11)[compute-0-3:30916] Signal code: Address not mapped (1)[compute-0-3:30916] Failing at address: 0x9a200b0[compute-0-3:30916] [ 0] /lib64/libpthread.so.0 [0x316940eb10][compute-0-3:30916] [ 1] /opt/bio/gromacs/lib/libgmx_mpi.so.6 [0x2b291ac0ee2c][compute-0-3:30916] *** End of error message ***--------------------------------------------------------------------------mpirun noticed that process rank 10 with PID 30916 on node compute-0-3.local exited on signal 11 (Segmentation fault).--------------------------------------------------------------------------* *Here is the mdp file:* *title = Martiniintegrator = mddt = 0.03 nsteps = 900000nstcomm = 100comm-grps = nstxout = 1000nstvout = 1000nstfout = 1000nstlog = 1000 ; Output frequency for energies to log file nstenergy = 100 ; Output frequency for energies to energy filenstxtcout = 1000 ; Output frequency for .xtc filextc_precision = 100xtc-grps = energygrps = HSPC CHOL Wnstlist = 10ns_type = gridpbc = xyzrlist = 1.4coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)rcoulomb_switch = 0.0rcoulomb = 1.2epsilon_r = 15 ; 2.5 (with polarizable water)vdw_type = Shift ;cutoff (for use with Verlet-pairlist) rvdw_switch = 0.9rvdw = 1.2 ;1.1 (for use with Verlet-pairlist);cutoff-scheme = verlet;coulomb-modifier = Potential-shift;vdw-modifier = Potential-shift;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity;verlet-buffer-drift = 0.005tcoupl = v-rescale tc-grps = HSPC CHOL Wtau_t = 1.0 1.0 1.0 ref_t = 323 323 323Pcoupl = berendsen ; parrinello-rahman ; parrinello-rahmanPcoupltype = isotropic ; semiisotropictau_p = 3.0 ; 12.0 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422compressibility = 3e-4 ; 3e-4ref_p = 1.0 ; 1.0 1.0gen_vel = yesgen_temp = 320gen_seed = 473529constraints = none constraint_algorithm = Lincscontinuation = nolincs_order = 4lincs_warnangle = 30* *I appreciate any help in advance.* -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.