On 24/03/2010 7:34 PM, Andrea Minoia wrote:
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
In the absence of information about your ensemble (from your .mdp file
or a description, hint hint) I'd guess it's because you've excluded all
the non-bonded interactions for which you had non-zero parameters defined.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
