[gmx-users] Some questions about free energy calculation
nicolis at guideo.fr
nicolis at guideo.fr
Tue Jan 15 19:04:17 CET 2002
Many thanks to both Davids :-) for the answers.
I am in the reading of a lot of papers.
Let me ask a little more questions as it is the first time I try the FEP
calculations.
I see in the literature that in general we equilibrate the system a few ps for
each lambda value and than collect the data for the averages.
In gromacs however, if I define a init_lambda, delta_lambda and nsteps, I
see that lambda changes by delta_lambda at each step, going from
init_lambda to init_lambda+delta_lambda*nsteps.
I understand that if I choose init_lambda=0 and delta_lambda=1/nsteps I
change from topology A to topology B, but without prior equilibration for
each lambda value and no "data collection" at each lambda. Is it a
different approach or it ends to the same DG if the delta_lambda is small
enough?
Is the DG the -kT ln<e^(E/kT)> computed by g_energy with the option -fee
for the dVpot/dlambda? And I have to apply the Born correction on that
value, am I correct?
And the -kT ln<e^(E/kT)> computed by g_energy with the option -fee for the
dEkin/dlambda should be zero?
Thanks again.
Yiannis
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