Dear Mark, Do you have any idea what's wrong with my simulation? You can find the mdp file and the description how I set up my system at the bottom of this email.
All the best! Dongsheng On Thu, 2006-07-06 at 19:16 -0400, Dongsheng Zhang wrote: > 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 _______________________________________________ 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
