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

[Andrea Minoia]

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
polymer

2) Create a new simulation file:    tpbconv  -s original.tpr -n index.ndx -o
rerun.tpr
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
Tot-Drift
------------------------------
-------------------------------------------------
Angle                       1630.18    61.5356    61.0703 -0.000872146
-26.1644
Ryckaert-Bell.              233.049    45.1358    34.5826 -0.00334919
-100.476
LJ-14                       669.907    20.0797    19.9169 -0.000294607
-8.8382
Coulomb-14                  637.187    16.2921    16.1707 0.000229164
6.87492
LJ (SR)                           0          0          0
0          0
Coulomb (SR)                      0          0          0
0          0
Potential                   3170.33    84.0654    75.4238 -0.00428678
-128.603


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
vacuo.
hope in some answers. Thanks

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100324/80b99a63/attachment.html>