**From:** Jerome Henin (*jhenin_at_cmm.chem.upenn.edu*)

**Date:** Mon May 11 2009 - 16:39:37 CDT

**Next message:**Fred (Rui FENG): "Calculating displacement in a system with periodic boundary"**Previous message:**Christopher Hartshorn: "FEP on 2.7b1"**In reply to:**yun luo: "Re: soft-core FEP in namd 2.7b"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
*

*>> >>>>
*

*>> >>>>
*

*>> >>>>
*

*>> >>>
*

*>> >>>
*

*>> >
*

*>> >
*

*>>
*

*>
*

*>
*

**Next message:**Fred (Rui FENG): "Calculating displacement in a system with periodic boundary"**Previous message:**Christopher Hartshorn: "FEP on 2.7b1"**In reply to:**yun luo: "Re: soft-core FEP in namd 2.7b"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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