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
--
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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