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

Andrea Minoia minoiaa at gmail.com
Wed Mar 24 09:34:59 CET 2010

Dear all,
I have performed a MD of a polymer chain interacting on a carbon nanotube
using gromacs 4.0.7. I need to evaluate the potential energy of the polymer
alone, during the dynamic, so to compare with its potential energy in vacuo.
During the dynamic, the CNT was frozen, and I used exclusions groups to
avoid to calculate CNT CNT non bonding interactions (I assume the bonds and
angles potentials are computed anyway).

Looking at the mailing list, I have used the following method:

1) use make_ndx to create a group system containing only the atoms for the

2) Create a new simulation file:    tpbconv  -s original.tpr -n index.ndx -o
3) adjust the trajectory according to the new simulation file:  trjconv -f
totaltrj.xtc -n index.ndx -s rerun.tpr -o rerun.xtc
4) analyze the trajectory: mdrun -s rerun.tps -rerun rerun.xtc

everything is performed without errors, but, when I use g_energy to evaluate
the energy of the polymer, I get something like:

Statistics over 15000001 steps [ 0.0000 thru 30000.0020 ps ], 7 data sets
All averages are over 15001 frames

Energy                      Average       RMSD     Fluct.      Drift
Angle                       1630.18    61.5356    61.0703 -0.000872146
Ryckaert-Bell.              233.049    45.1358    34.5826 -0.00334919
LJ-14                       669.907    20.0797    19.9169 -0.000294607
Coulomb-14                  637.187    16.2921    16.1707 0.000229164
LJ (SR)                           0          0          0
0          0
Coulomb (SR)                      0          0          0
0          0
Potential                   3170.33    84.0654    75.4238 -0.00428678

The question is: why the short range lennard-jones and short range coulombic
interactions are zero? those are the usual option from 1 to 8:
  2  Angle            3  Ryckaert-Bell.   4  LJ-14   5  Coulomb-14       6
LJ-(SR)          7  Coulomb-(SR)     8  Potential

They are present for the orginal dynamic on CNT as well as in the dynamic in
hope in some answers. Thanks

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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