Thank you Justin, is there a way I can choose both Protein LIG? It has the following options for me
Reading toplogy and shit from md.tpr Reading file md.tpr, VERSION 4.0.5 (single precision) 50000 steps (100 ps) remaining from first run. Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Group 0 ( System) has 37770 elements Group 1 ( Protein) has 3848 elements Group 2 ( Protein-H) has 1980 elements Group 3 ( C-alpha) has 244 elements Group 4 ( Backbone) has 732 elements Group 5 ( MainChain) has 974 elements Group 6 (MainChain+Cb) has 1206 elements Group 7 ( MainChain+H) has 1198 elements Group 8 ( SideChain) has 2650 elements Group 9 ( SideChain-H) has 1006 elements Group 10 ( Prot-Masses) has 3848 elements Group 11 ( Non-Protein) has 33922 elements Group 12 ( LIG) has 35 elements Group 13 ( SOL) has 33807 elements Group 14 ( Na) has 46 elements Group 15 ( Cl) has 34 elements Group 16 ( Other) has 33922 elements Select a group: On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > John Shultz wrote: >> >> I am trying to rerun a simulation using this command >> mdrun -rerun -v -deffnm md >> >> I think I must have made a mistake when I prepared the original mdp >> file because I get this message >> Number of atoms in trajectory (3883) does not match the run input file >> (37770) >> >> I have these files in my directory >> Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp >> md_prev.cpt md.tpr md.trr md.xtc traj.trr >> >> Here is my mdp file, should I remove entries for xtc_grps and >> energygrps to avoid this issue? >> > > You can, but it won't fix anything. Your original .xtc file saved only the > coordinates of the Protein and LIG (per your output options), but your .tpr > file has all of these atoms, regardless of what you choose to save. You > can, however, create a .tpr file that has a just these atoms by passing your > original .tpr file to tpbconv, using a suitable index group. > > -Justin > >> integrator = md >> nsteps = 50000 >> dt = 0.002 >> nstvout = 5000 >> nstlog = 500 >> nstenergy = 250 >> nstxtcout = 5000 >> nstxout = 5000 >> xtc_grps = Protein LIG >> energygrps = Protein SOL >> constraints = all-bonds >> nstcomm = 1 >> ns_type = grid >> rlist = 1.2 >> rcoulomb = 1.1 >> rvdw = 1.0 >> vdwtype = shift >> rvdw-switch = 0.9 >> coulombtype = PME-Switch >> Tcoupl = v-rescale >> tau_t = 0.1 0.1 >> tc-grps = protein non-protein >> ref_t = 300 300 >> Pcoupl = parrinello-rahman >> PcOupltype = isotropic >> tau_p = 0.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> gen_vel = yes >> lincs-iter = 2 >> DispCorr = EnerPres >> optimize_fft = yes >> gen_seed = 805087 > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
