From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon May 11 2009 - 16:39:37 CDT
Because their lambda means (1 - lambda). Both the article and the
user's guide clearly say what they mean by "lambda"... Unfortunately,
it's not the same thing.
On Mon, May 11, 2009 at 1:31 PM, yun luo <luoyun724_at_gmail.com> wrote:
> Hi, dear NAMD developers,
>
> I read the reference article about the soft-core method (JCP 1994). In the
> article, the form of shift parameter (fepVdwshiftCoeff) is r**2 +
> fepVdwshiftCoeff * lambda. But in NAMD2.7 document, it is r**2 +
> fepVdwshiftCoeff * (1-lambda). I'm wondering why this form need to be
> changed? Thanks!
>
> Ly
>
> On Sun, May 10, 2009 at 10:19 PM, Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
> wrote:
>>
>> > @Jerome:
>> > ok, the lambda=1 case is fine with me :-)
>> >
>> > however, for the lambda=0 case:
>> >
>> >> Lennard-Jones (and of course it goes to zero as lambda vanishes). So
>> >
>> > This is right for lambda_up_LJ, but what about lambda_down_LJ at
>> > lambda=0?
>>
>> Well, then lambda_down_LJ is equal to 1. Substitute in soft-core
>> potential, lather, rinse, repeat.
>>
>>
>> > a) is there simply no soft-core potential for the vanishing set of
>> > particles?
>>
>> They feel exactly the same potential, sampled along the same
>> pathway... in the opposite direction.
>>
>>
>> > b) the vanishing set of particles are not expected to have clashes
>>
>> Not when they *start* vanishing (lambda = 0), but they do when they
>> have almost completely vanished (lambda ~ 1).
>>
>>
>> > if a): @Chris: maybe one could stress explicitly what interactions (what
>> > with what) are considered for the soft-core potentials?
>>
>> All the LJ interactions affected by the scaling, that is (say we are
>> mutating group A into B in environment E):
>> 1) A <-> E
>> 2) B <-> E
>>
>> Plus, iff decouple is OFF:
>> 3) A <-> A
>> 4) B <-> B
>> (with decouple on, those interactions are not perturbed)
>>
>> Side note: normally there are no A <-> B interactions.
>>
>>
>> > if b): is "fepVdwShiftCoeff=5.0" a little high, considering that even
>> > non-clashing particles have distances of 3A or so?
>>
>> The shift applies to square distances and is given in A^2. The default
>> shifting distance is really sqrt(5) in Angstrom.
>>
>>
>> > Sorry, I lost the link to your original soft-core paper, if you could
>> > send
>> > it to me again?
>>
>> There (not ours, by the way):
>> http://link.aip.org/link/?JCPSA6/100/9025/1
>>
>> Cheers,
>> Jerome
>>
>>
>>
>> > Jerome Henin wrote:
>> >>
>> >> Hi Sebastian,
>> >>
>> >> 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.
>> >>
>> >> Best,
>> >> Jerome
>> >>
>> >> On Sun, May 10, 2009 at 11:36 AM, Sebastian Stolzenberg
>> >> <s.stolzenberg_at_gmail.com> wrote:
>> >>
>> >>>
>> >>> 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,
>> >>> Best,
>> >>> Sebastian
>> >>>
>> >>>
>> >>> Chris Harrison wrote:
>> >>>
>> >>>>
>> >>>> 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 <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,
>> >>>> Best,
>> >>>> Sebastian
>> >>>>
>> >>>>
>> >>>>
>> >>>
>> >>>
>> >
>> >
>>
>
>
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