On 14/03/11, "C.Y. Chang" <chiayun.ch...@gmail.com> wrote: > 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. >
There's good reasons for this. How would you define the "HB energy" in terms of the kind of information accessible to MD simulations? > 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 > Look up energy groups in the manual - start of section 3.3. Your .mdp file is defining an illegal combination of atoms and energy monitor 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? > An inter-group energy doesn't mean anything much, so don't bother. Please read the whole of this thread http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html Mark
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