Mark, Thank you very much for your reply. On Fri, 2006-07-07 at 08:51 +1000, Mark Abraham wrote: > > Hello, GMX users, > > > > My system exploded very soon after mdrun. So I outputted the log file > > every step. I found the initial temperature is about 800 K even though I > > set ref_T = 300. Why does this happen? > > First please tell us you've done energy minimization and checked the > structure and resulting trajectory visually to see that things look > reasonable there.
The following is the mdp file: ; VARIOUS PREPROCESSING OPTIONS title = nanotube_polymer - z T300 cpp = /lib/cpp -traditional include = define = ; RUN CONTROL PARAMETERS integrator = md tinit = 0 ; Start time and timestep in ps ;constraints = hbonds ; constrain bonds involving H. dt = 0.002 nsteps = 1000000 ;2 ns comm-mode = ANGULAR ;Linear nstcomm = 1 comm-grps = ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) ; this affects file "traj.trr" nstxout = 50000 nstvout = 50000 nstfout = 50000 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy = 1 energygrps = CNT polymer ; Output frequency and precision for xtc file (for the movie) nstxtcout = 1 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ; nblist update frequency ns_type = simple ; ns algorithm (simple or grid) pbc = no rlist = 0 ; nblist cut-off ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics: Cut-off, coulombtype = Cut-off fourierspacing = 0.12 pme_order = 4 rcoulomb = 0 optimize_fft = yes ;This saves a few percent for long simulations ;rcoulomb_switch = 0.95 ; Dielectric constant (DC) for cut-off or DC of reaction field ;epsilon-r = 1.0 ; for reaction field ; Method for doing Van der Waals vdw-type = cut-off ; cut-off lengths rvdw = 0 ;rvdw_switch = 0.95 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no; EnerPres ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; nose-hoover ;berendsen ; Groups to couple separately tc-grps = polymer CNT ; Time constant (ps) and reference temperature (K) tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling Pcoupl = no; berendsen ;Parrinello-Rahman ;berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 gen_seed = 1223188 ;Electric fields ;E_z = 1 40 1 My system is a carbone nanotube with a polymer. The polymer has 80 units. After I generated the polymer chain, I have relaxed the polymer alone in vacuum for 200 ps. Then I added CNT to the system, and made sure there was no overlap by VMD. Then I did EM in vacuum. I used the above mdp to generate a tpr file. When I ran it, the polymer exploded. However, If I simulate the polymer alone in vacuum, it works fine with the same force field. This problem sounds strange to me. How do you think? Best Wishes! Dongsheng > If so, and there are still problems you'll need to > supply a full .mdp and describe the simulation you're trying to run. > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
