Hi Justin, I have changed the value of nsteps(>100) and the nstout(=1), but I found that there is just the static figure and no animation .
it always shows that :Last frame 0 time 0.000 What is the problem? Thank you for your reply. Yang ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL PROTECTED] Sent: Monday, November 03, 2008 4:22 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the mdp file He, Yang wrote: > Hi all users, > > When I change the value of nsteps in my mdp file to run the gromacs and show > the trajectory in the gromcas, I found that only the value of nsteps is set > by 10, is there just the animation of the molecule's movement . I have tried > many time and set the other values of nsteps, there isn't any movement about > the molecule at all. > I'm not quite clear on what the problem is. But you should be aware that 10 steps (0.02 ps in your case!) is an exceedingly short timeframe under any circumstances. If what you've shown is your full .mdp file, then the other values will be taken as default. For output (nstxout) this value is 100. So you will likely only see the starting and ending coordinates of your 10-step simulation. Try a longer simulation (>100 steps) or specify nstxout = 1 and see if you generate 10 frames. -Justin > I am strange about that and this is my part of mdp file: > > ;VARIOUS PREPROCESSING OPTIONS > title = atom > ; Preprocessor - specify a full path if necessary. > cpp = cpp > define = > > ; RUN CONTROL PARAMETERS > integrator = md > ; Start time and timestep in ps > tinit = 0 > dt = 0.002 > nsteps = 10 > ; For exact run continuation or redoing part of a run > init_step = 0 > ; mode for center of mass motion removal > comm-mode = Linear > ; number of steps for center of mass motion removal > nstcomm = 1 > ; group(s) for center of mass motion removal > comm-grps = > > > > > ; NEIGHBORSEARCHING PARAMETERS > ; nblist update frequency > nstlist = 1 > ; ns algorithm (simple or grid)c 4 > ns_type = grid > ; Periodic boundary conditions: xyz (default), no (vacuum) > ; or full (infinite systems only) > pbc = xyz > ; nblist cut-off > rlist = 0.686 > domain-decomposition = no > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = User > rcoulomb-switch = 0 > rcoulomb = 0.9 > ; Relative dielectric constant for the Cut-off or DC of the reaction field > epsilon-r = 78 > ; Method for doing Van der Waals > vdw-type = User > ; cut-off lengths > rvdw-switch = 0 > rvdw = 0.9 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = EnerPres > ; Extension of the potential lookup tables beyond the cut-off > table-extension = 1 > ; Seperate tables between energy group pairs > energygrp_table = > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > > > Can anyone of you tell me what is the problem? > > Thank you very much. > > Yang > _______________________________________________ > 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 > -- ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ 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 _______________________________________________ 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