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: mino...@averell.umh.ac.be Tel: +32 65 373859 Fax: +32 65 373861
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