Re: soft-core FEP in namd 2.7b

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Fri May 08 2009 - 16:14:44 CDT

Sebastion,

Please look here to begin:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9953.html

C.

--
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 Fri, May 8, 2009 at 11:57 AM, Sebastian Stolzenberg <
s.stolzenberg_at_gmail.com> wrote:
> Dear All,
>
> I have some trouble interpreting the new parameters (listed below) in the
> namd 2.7b manual's FEP chapter.
> Here are my interpretations, I would be glad if you could check them with
> me:
>
> I assume that decouple is set to "on".
>
> manual p. 118:
> "fepVdwShiftCoeff / tiVdwShiftCoeff":
> considered are only vdW interactions between the growing/shrinking
> particles and their respective environments only.
> (otherwise: what's the use of soft-core for vdW of the environment with
> itself?)
>
> "fepElecLambdaStart/tiElecLambdaStart ":
> considered are only the elect. interactions of the growing particles with
> its environment:
> E_el(0.5)=0 linearly increased to E_el(1.0)=full strength
> (my thinking is that interactions between the shrinking particles with the
> environment are *decreasing*)
>
> p. 119:
> "fepVdwLambdaEnd / tiVdwLambdaEnd":
> it means that @lambda>0.5, we set fepVdwShiftCoeff (tiVdwShiftCoeff) to
> zero.
>
> Is this all correct?
> If yes, then @lambda=0, I see an abrupt transition from "hard-core" to
> "soft-core" for vdW interactions between shrinking particles and their
> environment.
> Is the corresponding free energy difference negligible with the default
> fepVdwShiftCoeff value of 5A^2? If not, how can one practically measure this
> free energy difference?
>
> Thank you,
> Best,
> Sebastian
>
>

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