From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Thu Mar 12 2009 - 18:51:05 CDT
I have an equilibrated NPT structure of a protein in explicit
lipid/solvent with periodic boundary conditions. Let's assume I do a
mutation R105A with dual-topology FEP. Certainly, I will also need to
transform a bulk water molecule (WAT) into a sodium (SOD) to keep the
net charge=0. To get the final free energy difference, I will subtract
delta_G(WAT->SOD) that I get from a separate run.
The system is large, I was thinking about fixing all atoms of the system
except for the ones around ~30A of the R105A mutation and the WAT->SOD
transformation. (Of course, I will not have a fixation boundary crossing
covalent bonds that leads e.g. to RATTLE constraint violations).
Is this feasible with NAMD-FEP? Any troubles with periodic boundary
conditions? I know that all could be locally done with implicit
lipid/solvent in CHARMM, which I would like to avoid for now.
Thanks so much,
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