In God We Trust Hello Dear gmx-users I performed MD simulation on Alcohol dehydrogenase for 1ns with time step 1fs and everything was ok.Becase of very slow speed of simulation I decided to increase the time step , then I took final structures (final gro and toplogy files) of this simulation and run another simulation with time step 2fs and the same parameters ,but after 109 ps I encounter with Segmentation fault ,even if I increase table-extention ,the result was the same. Here is my mdp file.
title = n.pdb restraining warnings = 10 cpp = /lib/cpp constraints = none integrator = md dt = 0.002 nsteps = 4850000 comm_mode = Linear nstcomm = 1 comm_grps = protein nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 250 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes table-extension = 2 ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = protein SOL CL- ref_t = 300 300 300 ; Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Would you please tell me what is wrong. Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/ _______________________________________________ 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
