From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sun May 10 2009 - 11:50:25 CDT
There is no need to neglect anything, the soft-core formalism is
analytically accurate. Have a look at the expression for the soft-core
potential and let lambda be 1: then it becomes identical to a 6-12
Lennard-Jones (and of course it goes to zero as lambda vanishes). So
switching from L-J to soft-core only changes the intermediate states 0
< lambda < 1, not the end-points of the calculation, hence it does not
change the (converged) free energy difference.
On Sun, May 10, 2009 at 11:36 AM, Sebastian Stolzenberg
> Thank you, Chris, I missed that link,
> theres is one more thing attracting my curiosity, the vdW
> hard-core<->soft-core transitions:
> 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?
> Thank you,
> 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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