[gmx-users] bonding energy

[Justin Lemkul]

On 3/14/13 4:08 PM, fatemeh ramezani wrote:
>
> I would check the energy connection between an amino acid and a ligand. After simulation, I run the following command:
>
> g_dist_mpi  -f   x.trr   -s  x.tpr   -n index.ndx -o pro.xvg
>
> Then I choose the bond  option (option 1)  from the  proposed options.
> Is this true for energy bonding finding between two molecules?
>

g_dist has nothing to do with bonds, so what you've posted doesn't make any sense.

There will be no "bonding energy" between two species that do not have actual 
chemical bonds defined in the topology, and even then, an .edr file (analyzed 
using g_energy) does not have decomposed bonding terms for individual 
interactions.  Gromacs just doesn't work like that.  You can get the sum of 
nonbonded interactions by setting appropriate energygrps in the .mdp file, and 
there are some rather complex methods for getting bonded energies (i.e. subset 
.tpr and .trr/.xtc, use mdrun -rerun on only those atoms of interest), but often 
such quantities are not particularly useful.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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