On 5/18/18 4:01 PM, Debdas Dhabal wrote:
Dear all,
I wonder if GROMACS has "energygrps" option (or any other similar options)
for bonded interactions (E_bond, E_ang, E_dih) for different groups. Let's
say I have three different chains in a single box and I want to extract the
bonded interactions for every chain separately. Would I be able to do that
on the fly during Gromacs run. I went through the webmanual and gmx_user
page but didn't find any solution for that. I would be very grateful if
someone could help me sharing how I could do this.
energygrps will do nothing for bonded terms.
If you want bonded energies of individual components, you will have to
strip out the coordinates you want from the trajectory (trjconv), make a
corresponding .tpr file (convert-tpr) and use mdrun -rerun to compute
the potential energy of that species. Note that these quantities are
quite unlikely to have any physical meaning.
-Justin
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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jalem...@vt.edu | (540) 231-3129
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