Contribution to potential energy by non-bonded interactions in protein-solvent system

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1

Hello everyone,

I am trying to simulate protein in a solvated environment with parallel strands of protein molecules. I am trying to compute the contribution of non-bonded interaction energy between proteins to the total potential energy of the system. Initially, I tried with "pe/atom" using the keywords pair and kspace, but according to the documentation provided it says "energy of each atom is due to its interaction with all other atoms in the simulation, not just with other atoms in the group." So the energy output of the syntax will be a combination of protein-protein and protein-water interactions.

Then I tried with group/group syntax which gives the total energy of interaction. So to obtain potential energy contribution, I subtracted the Kinetic energy of the protein atoms from the output. The output was coming quite absurdly high.

I would like to know can group/group command give the required output using the two groups as "protein" subtracting kinetic energy of the protein atoms. Or is there any other way to compute the non-bonded interactions between protein atoms?

2

have a look at the “rerun” command. you run your simulation with full interations once and record the trajectory, and then you use “rerun” on the same trajectory file and define only those interactions, you are interested in and thus can get any decomposition you want. that is, for pairwise additive interactions, so you better switch from long-range coulomb to cutoff coulomb with a sufficiently large coulomb cutoff, to have reasonably converged energies. since you are not using the computed forces, the error from cutoff coulomb is on the small side and doesn’t affect the trajectory by construction.

axel.