Hi Mark, Thanks for your reply!
I want to use the pre-saved trajectory. Based on the distance criteria, calculate the Coulomb and LJ interaction. However, I don't know the data structure related with the LJ parameters. Do you have related knowledge? The mdrun -rerun might be impossible for me, because I want to calculate the energy terms based on the distance, which is not the cutoff distance in the simulations, but one from RDF calculation. regards, Baofu Qiao Mark Abraham wrote: > On 08/02/10 21:03, Baofu Qiao wrote: >> Hi all, >> >> I want to calculate the non-bonded interactions (LJ+Coulomb) between two >> sub-groups when they are within the cutoff distance. The sub-groups are >> only parts of the whole energy groups used in my .mdp file. Given the >> partial charges of the atoms involved are easy to get from the >> "top.atoms.atom[index[i]].q", I have no idea how to get the LJ >> parameters of the atoms? >> >> Does anyone know how to get them from the top.atoms.atomXXX? Or is there >> some similar code to calculate such energies? > > If you want them calculated mid-simulation, then you'll have to find > the relevant data structure. > > Otherwise, define useful energy groups, and calculate the terms from > frames in a saved trajectory using mdrun -rerun. Get the data from the > resulting .edr with g_energy in the usual way. > > 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
