Mark, thank you for the fast reply. My original mdp, the one I used to run the dynamics is
nstcgsteep = 1000 nbfgscorr = 10 emstep = 0.02 emtol = 10 dt = 0.002 nsteps = 15000000 comm-mode = none nstcomm = 1 comm_grps = system nstxout = 1000 nstvout = 1000 nstfout = nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc_grps = system energygrps = CNT pcl nstlist = 10 ns_type = grid pbc = xyz rlist = 1.5 coulombtype = cut-off rcoulomb = 1.5 vdwtype = cut-off rvdw = 1.5 periodic_molecules = yes tcoupl = nose-hoover tc-grps = system tau_t = 0.5 ref_t = 300 Pcoupl = no pcoupltype = isotropic tau_p = 5.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no gen_temp = 300 gen_seed = -1 constraints = all-bonds constraint_algorithm = LINCS lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 freezegrps = CNT freezedim = Y Y Y nwall = 0 wall_type = 9-3 wall_r_linpot = -1 wall_atomtype = wall_density = wall_ewald_zfac = 3 ewald_geometry = 3d energygrp_excl = CNT CNT with this I have created, of course the tpr used to run the dynamic: runmd.tpr. With make_ndx, I have an index file containing only the pcl group. using this index file, i have created the new tpr, rerun.tpr, from the original runmd.tpr file using tpbconv. as far as I see, the only exclusion is for the CNT CNT groups (last line of the mdp file above). a gmxdump of rerun.tpr gives me this info about groups (at the end of the file) Group statistics T-Coupling : 756 (total 756 atoms) Energy Mon. : 756 0 0 (total 756 atoms) Acceleration: 756 (total 756 atoms) Freeze : 756 0 (total 756 atoms) User1 : 756 (total 756 atoms) User2 : 756 (total 756 atoms) VCM : 756 (total 756 atoms) XTC : 756 (total 756 atoms) Or. Res. Fit: 756 (total 756 atoms) QMMM : 756 (total 756 atoms) If this is not helping you, please can you tell me what else you need? Again, thanks. cheers, Andrea In the absence of information about your ensemble (from your .mdp file or a > description, hint hint) I'd guess it's because you've excluded all the > non-bonded interactions for which you had non-zero parameters defined. > > Mark > -- > 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 > -- Dr. Andrea Minoia Chemistry of Novel Materials Uneversity of Mons, UMONS Parc Initialis, Avenue Copernic 1 B-7000 Mons, Belgium Mail: mino...@averell.umh.ac.be Tel: +32 65 373859 Fax: +32 65 373861
-- 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