Hi All, I'm conducting a simulation of insulin unfolding in water for a long period of time (20 ns or more). There were approximately 7800++ SOL molecules in the system. I'm using tip4p water molecules to solvate my system.
I intend to generate only the trajectories of my protein alone, without outputing trajectories of the solvents. This is since the output files can get really massive. So looking at the manual, I've inserted the line: "xtc_grps = Proteins" into the .mdp input file and did a short simulation to try it out. However, after the run I've examined the .g96, .xtc, .trr, etc.. files and found that the whole system (Protein + SOL) were outputted, instead of just the Protein itself. I've also tried generating my own index file to feed into grompp, but that didn't help either. What could be the plausible problem? I'm currently using Gromacs/3.3.3. Thanks for the advise. Attached below is a cut&paste of my .mdp input file for the simulation. -Wade ================================================= title = Molecular dynamics simulation at 500K cpp = /usr/bin/cpp integrator = md dt = 0.001 nsteps = 1000 nstcomm = 10 comm-mode = Linear xtc_grps = Protein nstxout = 50 nstvout = 50 nstfout = 0 nstxtcout = 50 nstlog = 50 nstenergy = 50 nstlist = 10 ns_type = grid pbc = xyz coulombtype = pme rlist = 1.0 rcoulomb = 1.0 vdw-type = Cut-off rvdw = 1.0 pcoupl = Berendsen pcoupltype = isotropic tau_p = 4.0 compressibility = 4.5e-5 ref_p = 1.0 Tcoupl = Berendsen tc_grps = System tau_t = 2.0 ref_t = 450. gen_vel = no gen_seed = 94839 constraints = All-bonds constraint-algorithm = lincs ================================================= _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
