[gmx-users] Some questions about free energy calculation

David L. Bostick dbostick at physics.unc.edu
Tue Jan 15 19:37:26 CET 2002


That is something the other David may be able to answer with more
confidence.  I have always been unsure of this.  So, I can offer the
following 2 cents..  In the past, I have always taken the dgdl.xvg file
output by doing FEP with mdrun, transformed the x-axis from units of time
to units of lambda, and integrated it numerically just to be on the safe


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

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?
> 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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list