I found something:<br><br>apparently, I need to remove the energygrp_excl = CNT CNT from the original mdp, generate a new tpr with this modified mdp and grompp, and then use tpbconv to create the simulation file for the subsystem. <br>
<br>my energy groups are still CNT and pcl and now g_energy gives something like this:<br><br>LJ (SR) -749.546 82.9686 63.7099 0.00613714 184.114<br>Potential 2214.7 89.2751 89.1628 0.000516773 15.5032<br>
LJ-SR:pcl-pcl 0 0 0 0 0<br><br>but still, LJ-SR:pcl-pcl is 0... should not be the same as LJ(SR)?... does not make too much sense. <br><br>Summarizing what i did:<br>
1) edit the mdp file, remove the groups in energygrp_excl, even if not used in the subsytem<br> Just to clarify, comparing the new mdp with that posted before, the only difference is:<br> < energygrp_excl = <br>
---<br> > energygrp_excl = CNT CNT<br><br>2) create the index file for the subsystem<br>
<br>3) rerun grompp to create the new tpr for all the system, without energygrp_excl<br>
<br>4) use the new tpr with tpbconv to create the simulation file for the subsystem<br>
<br>5) adjust the trajectory<br>
<br>6) run mdrun -rerun<br>
<br>andrea<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>