[gmx-users] extract subsystem energy: problem with mdrun -rerun and LJ(SR)

Andrea Minoia minoiaa at gmail.com
Wed Mar 24 11:02:57 CET 2010

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

LJ (SR)                    -749.546    82.9686    63.7099 0.00613714
Potential                    2214.7    89.2751    89.1628 0.000516773
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

4) use the new tpr with tpbconv to create the simulation file for the

5) adjust the trajectory

6) run mdrun -rerun

Dr. Andrea Minoia
Chemistry of Novel Materials
Uneversity of Mons, UMONS
Parc Initialis, Avenue Copernic 1
B-7000 Mons, Belgium
Mail: minoiaa at averell.umh.ac.be
Tel: +32 65 373859 Fax: +32 65 373861
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