[gmx-users] Segmentation fault error

[Seyed Mojtaba Rezaei Sani]

*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)