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

[Andrea Minoia]

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: minoiaa at averell.umh.ac.be
Tel: +32 65 373859 Fax: +32 65 373861
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