[gmx-users] Some questions about free energy calculation
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jan 15 19:29:40 CET 2002
On Tue, 15 Jan 2002 nicolis at guideo.fr wrote:
>
>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?
It is better to set init_lambda to a distinct number of values (say 21, 0,
0.05, 0.1 .. 1.0) and delta_lambda to 0.0. You then do each run for say
200 ps and check the curves of dV/dlambda (extract them with g_energy).
You can for each point separately determine average and std. dev. and
check equilibration. If you do 200 ps, you can e.g. use the first 50 ps as
equilibration.
>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?
You have to integrate the points manually (or e.g. using xmgrace).
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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