[gmx-users] T->A mutation for a dimer protein

[chris.neale at utoronto.ca]

Dear Lishan:

First, it would be great to see some evidence that you have tried to  
do this yourself before posting. Your "I think" makes it a possible  
waste of time for us to suggest a resolution to a problem that may or  
may not exist.

Second, if indeed it is a problem, perhaps you could use two identical  
topologies with different molecule names and treat them separately.

Chris

-- original message --

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?

Best,
Lishan