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On 23/06/2011 9:48 AM, <a class="moz-txt-link-abbreviated" href="mailto:yaolisha@msu.edu">yaolisha@msu.edu</a> wrote:
<blockquote cite="mid:20110622194857.19470luoroatmmax@mail.msu.edu"
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<p class="MsoNormal"><span lang="EN-US">Hi All,<br>
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? <br>
</span></p>
</blockquote>
<br>
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?<br>
<br>
Mark<br>
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