Hi, I try to calculate hydrogen bond (HB) energy. The g_energy does not have this term. And I find the g_hbond function in Gromacs. But the HB energy calculation is not in g_hbond. Therfore, I also try to dump the .ndx file including the HB_donor, HB_acceptor and HB_system from g_hbond, and perfrom the grompp But there is a error msg,
Atom 17380 in multiple Energy Mon. groups Another problem is about calculating the intramolecular energy e.g. 1,4-nonbonded, van der waal, electrostatic etc. of the ligand in lipid layer-ligand complex system. I could set up the energy_grp and calculate energy between the ligand group and the lipid layer group. But I need the intramolecular energy in the groups. How should I deal with these problems? Best, Chia-yun Chang
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