From: yun luo (luoyun724_at_gmail.com)
Date: Mon May 11 2009 - 12:31:49 CDT
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> <
> 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
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >
> >
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:46 CST