On 5/12/2011 12:17 AM, Vasileios Tatsis wrote:
Greetings GrOmAcS Users,
I want to calculate the free energy, for different (de)protonation
states, of a certain compound.
This requires to edit by hand many topology files.
Is there a code that can do it on-the-fly or any ideas(algorithm) how
it can be done automatically?
Since you'd need to add/remove the proton and perhaps change the atom
type to which it was bound and maybe its other proton atom types, it is
hard to come up with a general algorithm that is worth the time to
implement.
Mark
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