On 23/06/2011 12:22 PM, Lishan Yao wrote: > Dear Chris and Mark, > Thank you both for the response. I did the simulation already and > Gromacs only gives me the total dH/dl.
So what's wrong with dividing by two, like I suggested last time? You've got two events and you assert that they're independent, so the statistics should be easy. --- I want an error estimation of the free energy change. not sure how if I only know the sum of the two. > The two mutated sites are more than 20A alway from each other which makes > it safe to assume that the interaction between the two sites is small. If I > can extract dH/dl for each site, I could get a resonable error estimation of > my calculation. Furthermore, if this is reliable I will do different > mutations in two monomers (as long as they are away from each other) so that > I can save my computational time by 50%. I guess this will involve some code > change. To which mutation would you assign the energy contribution of the atoms around half way between them? --- I do not intend to assign energy contribution to each surrounding atom. Gromacs gives dH/dl = dH/dl (monomer 1 site) + dH/dl (monomer 2 site). My question is whether it is possible to extract dH/dl (monomer 1 site) and dH/dl (monomer 2 site) separately. I would think it should be straightforward practically. Best, Lishan Mark > Best, > Lishan >
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