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 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 [email protected] 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
