**From:** Chris Harrison (*charris5_at_gmail.com*)

**Date:** Wed Jul 29 2009 - 06:11:33 CDT

**Next message:**Chris Harrison: "Re: Re: THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active"**Previous message:**Eric Perim: "Different ensembles in the same system"**In reply to:**Dan Bolintineanu: "FEP implementation in NAMD 2.6 vs. 2.7b1"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dan,

To add to Floris' comment, you are seeing the non-physical path resulting

from the softcore potential as described by Zacharias, in which

electrostatics and vdW are independently decoupled from the MD potential.

Please look at the decoupling schemes figure in the FEP section of the

manual. As you will see there is a type of minimum at lambda=0.5 where

electrostatics for both incoming and outgoing partitions are at a minimum;

and vdW for both partitions are at the lowest values possible for

*both*partitions

*at the same time* *(or lambda value)*. This "middle-point" corresponds to

the "inflection point" in your non-physical path. The rest should be fairly

obvious; please let us know if not. We'd be happy to try and help clarify.

WRT the difference between 2.6 and 2.7b1, I suggest, off the cuff, that this

is due to the lack of a softcore potential in 2.6 and that as you increase

the number of non-linear windows as you approach lambda values of 0 or 1, I

suspect your dG will approach 0 .... as it does in the case of softcore with

2.7b1's value of -0.002.

Chris

-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Tue, Jul 28, 2009 at 4:50 PM, Dan Bolintineanu < dan.bolintineanu_at_gmail.com> wrote: > Hi all, > > I've been trying to do some FEP calculations using NAMD, and have been > experimenting with the ethane-ethane zero-sum calculation in the NAMD > FEP tutorial to get a feel for FEP calculations. I found the results > a bit surprising, and was hoping someone could shed some light on > them. > > Using NAMD 2.7b1 with > fepElecLambdaStart 0.5 > fepVdwLambdaEnd 1.0 > decouple on > I obtain a satisfactory final result, about -0.002 kcal/mol. However, > the lambda vs. delta G plot looks nothing like the one in the > tutorial; it decreases linearly to about -7 kcal/mol, after which it > increases linearly to -0.002 kcal/mol. > > In NAMD 2.6, using the exact same input file and sampling strategy, > but commenting out the three lines above, I obtain a final result of > +0.2 kcal/mol, but a delta G plot that seems much more reasonable, > very similar to the one in the tutorial (except for the endpoint). > > In both cases, I have used much higher sampling (larger # of windows) > than indicated in the FEP tutorial. I've attached my input file for > the NAMD 2.7b1 run. > > My questions are: > 1.) Why does the NAMD 2.6 final result not coincide with the one in > the FEP tutorial? > 2.) Why does the NAMD 2.7b1 lambda vs. dG curve look so strange, and > is the result valid in spite of this? > > Thanks in advance. > > Dan Bolintineanu >

**Next message:**Chris Harrison: "Re: Re: THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active"**Previous message:**Eric Perim: "Different ensembles in the same system"**In reply to:**Dan Bolintineanu: "FEP implementation in NAMD 2.6 vs. 2.7b1"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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