GROMACS version: 4.5.5
GROMACS modification: No
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I have some queries regarding calculating electrostatic energy values for simulated protein. It would be very great if you could help in this regard.
I have two protein systems (one wild type and another mutant) simulated using gromacs package. I wanted to check if there are any energy differences occurred due to mutation. So I rerun the system with mdrun -rerun and calculated Coul-SR energy values over simulation time for some specific residue pairs from both systems. And I observed as, there were some differences in the values.
Does this “Coul-SR” takes care of the environmental effect in the calculations, implicitly? or how?
As there are point charges (q1,q2, r=distance between them) allotted to each atom and they do not change. q1q2/square®. How the environment effect is considered?
or the differences are occurring due to the dynamics of the protein? i.e. it is just dependent on ® distance between residue pair?
Also, how does it consider the water effect? If water molecules are interacting with residues and if I calculate Coul-SR energy between those residue pairs.
I understood that with rerun I’ll be recalculating the energy terms for existing frames.
What I havn’t understood is, ‘changes in coulomb energy are due to partial charge i.e diffenece in topology’.
I have a concern regarding the environmental effect on Coul-SR energy calculations.
Let say if I have system of 2 amino acids simulated in vaccume envionment and in water solvated enevironment. (assuming distance between them is not much changing in the simulations)
So question I have is that, will there be any difference in the Coul-SR values for the same pair of aminoacids if computed in vaccume versus computed in the solvated state.
As these values will be explicitly calculated from the point charges, So should we expect any difference in the values? or if any differences occuring from the environment?
If you have species A and B separated by some distance, and you compute their interaction energy, the value will be the same in vacuum or if you have water molecules between them. This is the essence of nonpolarizable (additive) force fields - there is no multibody effect. You simply get a pairwise decomposition of the potential energy. Breaking this interaction energy down further into LJ and electrostatic components is largely meaningless because force fields are not parametrized in such a way that these quantities are physically useful.