[gmx-users] Energy calculation

Mark Abraham mark.abraham at anu.edu.au
Mon Mar 14 10:28:08 CET 2011

On 14/03/11, "C.Y. Chang"  <chiayun.chang at 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

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