[gmx-users] Energy calculation

[C.Y. Chang]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110314/9d42663a/attachment.html>