hello sir,<br><br>thanks for your kind reply..<br><br>in another folder i resubmitted my mdrun from starting time..<br><br>i reduced my time step..<br>i kept my time step = 0.001<br> <br><br>this is my md.mdp file<br><br>title = Gromacs43a1 lipopeptide MD <br>
; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 5000000 ; 1 * 5000000 = 5000 ps, 5 ns<br>dt = 0.001 ; 1 fs<br>; Output control<br>nstxout = 1000 ; save coordinates every 2 ps<br>
nstvout = 1000 ; save velocities every 2 ps<br>nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps<br>nstenergy = 1000 ; save energies every 2 ps<br>nstlog = 1000 ; update log file every 2 ps<br>
; Bond parameters<br>continuation = yes ; Restarting after NPT <br>constraint_algorithm = lincs ; holonomic constraints <br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>lincs_iter = 1 ; accuracy of LINCS<br>
lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br>ns_type = grid ; search neighboring grid cells<br>nstlist = 5 ; 10 fs<br>rlist = 1.4 ; short-range neighborlist cutoff (in nm)<br>
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)<br>rvdw = 1.4 ; short-range van der Waals cutoff (in nm)<br>; Electrostatics<br>coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics<br>
pme_order = 4 ; cubic interpolation<br>fourierspacing = 0.16 ; grid spacing for FFT<br>; Temperature coupling is on<br>tcoupl = <b>V-rescale</b> ; modified Berendsen thermostat<br>tc-grps = DRG SOL ; two coupling groups - more accurate<br>
tau_t = 0.1 0.1 ; time constant, in ps<br>ref_t = 300 300 ; reference temperature, one for each group, in K<br>; Pressure coupling is on<br>pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<br>
pcoupltype = isotropic ; uniform scaling of box vectors<br>tau_p = 2.0 ; time constant, in ps<br>ref_p = 1.0 ; reference pressure, in bar<br>compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1<br>
; Periodic boundary conditions<br>pbc = xyz ; 3-D PBC<br>; Dispersion correction<br>DispCorr = EnerPres ; account for cut-off vdW scheme<br>; Velocity generation<br>gen_vel = no ; Velocity generation is off <br>
<br><br>i resubmitted my mdrun and my run completed i analysed my output file..<br><br>now it completed at 1.286ns out of 5ns..<br><br>in log file it didnt give any information about this error..<br><br>in error file its showing segmentation fault..<br>
<br><br>how to solve this prolem..<br><br>is it only because of some problem in my system??<br><br>thanking you.<br><br>