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