[gmx-users] Energy calculation
chiayun.chang at gmail.com
Mon Mar 14 09:35:46 CET 2011
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?
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