On 23/06/2011 9:48 AM, yaoli...@msu.edu wrote:
Hi All,
I have a protein dimer and I want to calculate a T to A mutation free
energy change using TI method. Since it is a dimer, it is very
convenient (and advantageous) to mutate the T in both monomer
simultaneously. Gromacs will write out dH/dl sum for the two mutations
together, I think. My question is how can I change Gromacs so than
dH/dl for T->A mutation in each monomer is written out separately?
You can't, because both have contributions from all the interactions. If
your method is sound, i.e. both mutations can take place without
affecting the other (big assumption IMO), surely you can just halve
dH/dl from the combined mutation to get the single-mutation dH/dl?
Mark
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