[gmx-users] free energy calculation in a big system

[Markus O Kaukonen]

Dear All,

Never done any free energy calculation with a computer, so... :

Is it possible (cpu and otherwise) to do a free energy calculation for a
system like in the manual (v 3.2 manual) page 36, fig. 3.9 case B
ie. two different inhibitors (I and I') docking the same enzyme (E)
when I and I' differ by one H+ (and the partial charges in I and I' are
different).

I (one system) and I' (the other system) have about 200 atoms and
E has 70000 atoms.

It seems at least that one has to do lot of things by hand in the topology
file (for things related to those 200 atoms).

Terveisin, markus.kaukonen at iki.fi

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