<br><br><div class="gmail_quote">Mark,<br>thank you for the fast reply. My original mdp, the one I used to run the dynamics is<br><br>nstcgsteep = 1000<br>nbfgscorr = 10<br>emstep = 0.02<br>
emtol = 10<br>dt = 0.002<br>nsteps = 15000000<br>comm-mode = none<br>nstcomm = 1<br>comm_grps = system<br>nstxout = 1000<br>
nstvout = 1000<br>nstfout =<br>nstlog = 1000<br>nstenergy = 1000<br>nstxtcout = 1000<br>xtc_grps = system<br>energygrps = CNT pcl<br>
nstlist = 10<br>ns_type = grid<br>pbc = xyz<br>rlist = 1.5<br>coulombtype = cut-off<br>rcoulomb = 1.5<br>vdwtype = cut-off<br>
rvdw = 1.5<br>periodic_molecules = yes<br>tcoupl = nose-hoover<br>tc-grps = system<br>tau_t = 0.5<br>ref_t = 300<br>Pcoupl = no<br>
pcoupltype = isotropic<br>tau_p = 5.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>gen_vel = no<br>gen_temp = 300<br>gen_seed = -1<br>
constraints = all-bonds<br>constraint_algorithm = LINCS<br>lincs-order = 4<br>lincs-iter = 1<br>lincs-warnangle = 30<br>freezegrps = CNT<br>freezedim = Y Y Y<br>
nwall = 0<br>wall_type = 9-3<br>wall_r_linpot = -1<br>wall_atomtype =<br>wall_density =<br>wall_ewald_zfac = 3<br>ewald_geometry = 3d<br>
energygrp_excl = CNT CNT<br><br>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.<br>
as far as I see, the only exclusion is for the CNT CNT groups (last line of the mdp file above).<br><br>a gmxdump of rerun.tpr gives me this info about groups (at the end of the file)<br><br>Group statistics<br>T-Coupling : 756 (total 756 atoms)<br>
Energy Mon. : 756 0 0 (total 756 atoms)<br>Acceleration: 756 (total 756 atoms)<br>Freeze : 756 0 (total 756 atoms)<br>User1 : 756 (total 756 atoms)<br>User2 : 756 (total 756 atoms)<br>
VCM : 756 (total 756 atoms)<br>XTC : 756 (total 756 atoms)<br>Or. Res. Fit: 756 (total 756 atoms)<br>QMMM : 756 (total 756 atoms) <br><br>If this is not helping you, please can you tell me what else you need?<br>
Again, thanks.<br>cheers,<br>Andrea<br><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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.<br>
<br>
Mark<br><font color="#888888">
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</font></blockquote></div><br><br clear="all"><br>-- <br>Dr. Andrea Minoia<br>Chemistry of Novel Materials<br>Uneversity of Mons, UMONS<br>Parc Initialis, Avenue Copernic 1<br>B-7000 Mons, Belgium<br>Mail: <a href="mailto:minoiaa@averell.umh.ac.be">minoiaa@averell.umh.ac.be</a><br>
Tel: +32 65 373859 Fax: +32 65 373861<br>