Hello Dear users, I appreciate your help with the following issues.
I am trying to extract interaction energies (non bonded) between hexane molecules (vdw and electrostatics). I have used rerun program to exclude intramolecular non bonded terms. In litrature people calculate these energies from vdw and electrostatics but still I do not have a clear image on details of energy contributions. In GROMACS thre are good many options like SR, LR (PME/ dis correction). 1-Can you please guide me for my hydrocarbon system what would be the best approach to get interaction energies? below are the enrgy terms I have at the moment. Do I need to include disp. corrections as well? Please help me with excluding or includeing PME and disp.corr contributions. Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------ Angle 4400.09 Ryckaert-Bell. 1009.62 LJ-14 648.411 Coulomb-14 -278.654 LJ (SR) -3010.16 Coulomb (SR) 74.7846 Coul. recip. -78.0436 Potential 2766.05 2- I have use nrexcl 7 in top file but I am still getting 1-4 interactions in breakdown! why is this heppening? 3- To calculate interaction energies can I sum up the energy contributions ? for example LJ-14 648.411 + Coulomb-14 -278.654 +LJ (SR) -3010.16 +Coulomb (SR) 74.7846 =... 4- About viewing the results: How can I plot the energy or force... vs. time ( graph)? I have found the program g_traj but it just lists the values ..no graph...! Thank you for your time :) MOeed
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