Dear all,<br>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).<br>
<br>Looking at the mailing list, I have used the following method:<br><br>1) use make_ndx to create a group system containing only the atoms for the polymer<br><br>2) Create a new simulation file: tpbconv -s original.tpr -n index.ndx -o rerun.tpr<br>
3) adjust the trajectory according to the new simulation file: trjconv -f totaltrj.xtc -n index.ndx -s rerun.tpr -o rerun.xtc<br>
4) analyze the trajectory: mdrun -s rerun.tps -rerun rerun.xtc<br><br>everything is performed without errors, but, when I use g_energy to evaluate the energy of the polymer, I get something like:<br><br>Statistics over 15000001 steps [ 0.0000 thru 30000.0020 ps ], 7 data sets<br>
All averages are over 15001 frames<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>------------------------------<div id=":9b" class="ii gt">-------------------------------------------------<br>
Angle 1630.18 61.5356 61.0703 -0.000872146 -26.1644<br>
Ryckaert-Bell. 233.049 45.1358 34.5826 -0.00334919 -100.476<br>LJ-14 669.907 20.0797 19.9169 -0.000294607 -8.8382<br>Coulomb-14 637.187 16.2921 16.1707 0.000229164 6.87492<br>
LJ (SR) 0 0 0 0 0<br>Coulomb (SR) 0 0 0 0 0<br>Potential 3170.33 84.0654 75.4238 -0.00428678 -128.603<br clear="all">
<br><br>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:<br> 2 Angle 3 Ryckaert-Bell. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Coulomb-(SR) 8 Potential <br>
<br>They are present for the orginal dynamic on CNT as well as in the dynamic in vacuo.<br>hope in some answers. Thanks<br><br>Andrea<br><font color="#888888">-- <br>
Dr. Andrea Minoia<br>Chemistry of Novel Materials<br>Uneversity of Mons, UMONS<br>Parc Initialis, Avenue Copernic 1<br>B-7000 Mons, Belgium<br>Mail: <a href="mailto:minoiaa@averell.umh.ac.be" target="_blank">minoiaa@averell.umh.ac.be</a><br>
Tel: +32 65 373859 Fax: +32 65 373861</font></div>