From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sun May 10 2009 - 10:36:47 CDT
Thank you, Chris, I missed that link,
theres is one more thing attracting my curiosity, the vdW
The real vdW potential is hard-core, but NAMD2.7b FEP can use soft-core.
Can one really neglect \delta_G from a hard-core<->soft-core transition?
How could one measure \delta_G and thus convince oneself in practice?
Chris Harrison wrote:
> Please look here to begin:
> 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 <mailto:char_at_ks.uiuc.edu>
> Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
> On Fri, May 8, 2009 at 11:57 AM, Sebastian Stolzenberg
> <s.stolzenberg_at_gmail.com <mailto: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,
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