From: yun luo (luoyun724_at_gmail.com)
Date: Tue May 05 2009 - 11:49:06 CDT
However, in the NAMD2.7 UserGuide, both fepVdWLambdaEND and
fepEleLambdaStart have default value 0.5. So I guess if we don't specify
those two value, the decoupling or coupling of VdW interaction will only be
carried out from lambda 0 to 0.5, and decoupling or coupling of
Electrostatic interaction will only be carried out during lambda 0.5 to 1.
Is that right?
On Tue, May 5, 2009 at 10:43 AM, Jerome Henin <jhenin_at_cmm.chem.upenn.edu>wrote:
> Hi all,
>
> Since this issue has been confusing to many people, here is a figure
> illustrating two common types of calculations, and what happens to the
> various coupling/decoupling parameters.
>
> Cheers,
> Jerome
>
>
> On Tue, May 5, 2009 at 11:18 AM, daniel aguayo <bioquimico_at_gmail.com>
> wrote:
> > Tks Chris for your answer. I now understand the meaning of it.
> >
> > Best
> >
> > Daniel Aguayo V.
> >
> > On Mon, May 4, 2009 at 11:24 PM, Chris Harrison <char_at_ks.uiuc.edu>
> wrote:
> >>
> >> Daniel,
> >>
> >> fepVdwLambdaEnd is the lambda value at which the coupling/decoupling of
> >> vdW interactions is desired to be completed. The default is 1.0, so the
> vdW
> >> interactions of annihilated atoms are gradually decoupled from a system
> from
> >> lambda=0 to lambda=1. In complimentary fashion, the vdW interactions of
> >> appearing atoms are gradually coupled to a system from lambda=0 to
> >> lambda=1.
> >>
> >> fepElecLambdaStart in a similar fashion controls the electrostatic
> >> coupling/decoupling. The default is 0.5, which results in the
> electrostatic
> >> interactions of annihilated atoms being gradually attenuated from
> lambda=0
> >> to lambda=0.5 as they are decoupled from the system, while electrostatic
> >> interactions involving appearing atoms are gradually coupled to the
> system
> >> from lambda 0.5 to 1.0.
> >>
> >> A value of 0.5 is perhaps not the best example to use, but does this
> >> answer your question?
> >>
> >>
> >> 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 Voice: 217-244-1733
> >> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
> >>
> >>
> >>
> >> On Mon, May 4, 2009 at 7:53 PM, daniel aguayo <bioquimico_at_gmail.com>
> >> wrote:
> >>>
> >>> Hi Jerome, can you explain more on the use of this new parameters
> >>> fepElecLambdaStart and fepVdwLambdaEnd
> >>>
> >>> Tks
> >>>
> >>> Daniel Aguayo V.
> >>> CBSM UTAL
> >>> Chile
> >>>
> >>>
> >>> On Mon, May 4, 2009 at 6:39 PM, Jerome Henin <
> jhenin_at_cmm.chem.upenn.edu>
> >>> wrote:
> >>>>
> >>>> Hi,
> >>>> As you said, the only reason why the dummy atom is needed is because
> >>>> NAMD 2.6 does not have soft-core potentials. The purpose of the
> >>>> tutorial is somewhat academic, in that the "charging free energy" is
> >>>> only meaningful within some theories of ion solvation, and is not an
> >>>> experimental observable.
> >>>> If you want a complete solvation free energy, then it is not necessary
> >>>> to follow the tutorial's "pseudo-single topology" approach.
> >>>>
> >>>> Note that if for some reason, you do want to use a dummy atom, its
> >>>> mass will not affect the thermodynamics of the system. It should
> >>>> typically not be less than 1.0, otherwise you may need to use smaller
> >>>> timesteps to preserve the stability of the simulation.
> >>>>
> >>>> One more remark: even the charging free energy can now be computed
> >>>> without the help of a dummy atom, since NAMD 2.7b1 allows for the
> >>>> separate decoupling of electrostatic and L-J interactions, through the
> >>>> fepElecLambdaStart and fepVdwLambdaEnd parameters.
> >>>>
> >>>> Best,
> >>>> Jerome
> >>>>
> >>>> On Mon, May 4, 2009 at 5:24 PM, yun luo <luoyun724_at_gmail.com> wrote:
> >>>> > Hi Chris,
> >>>> >
> >>>> > Thank you for your reply.
> >>>> > Actually, I did follow the FEP tutorial part 2. Charging a spherical
> >>>> > ion
> >>>> > using dual-topology paradigm. That's why I want add a dummy atom. In
> >>>> > the
> >>>> > tutorial one adds a dummy atom with 0 charge but the same radius as
> >>>> > sodium
> >>>> > because there is no soft-core contribution in NAMD2.6. Since NAMD2.7
> >>>> > has
> >>>> > soft-core part, I think I need using a dummy atom with 0 charge 0
> >>>> > radius to
> >>>> > get both elec and vdW energy. But do you think the a dummy atom with
> >>>> > nonzero
> >>>> > mass will cause problem?
> >>>> >
> >>>> > Many thanks!
> >>>> >
> >>>> > On Mon, May 4, 2009 at 3:33 PM, Chris Harrison <char_at_ks.uiuc.edu>
> >>>> > wrote:
> >>>> >>
> >>>> >> Ly,
> >>>> >>
> >>>> >> With 0 charge, 0 mass, and 0 radius the dummy particle is
> effectively
> >>>> >> the
> >>>> >> same as no atom .... which is of course the desired effect usually.
> >>>> >> Assuming you're not doing something unusual, then you don't need
> the
> >>>> >> dummy
> >>>> >> particle. You should be able to just make the Na disappear.
> >>>> >>
> >>>> >> The FEP tutorial may be of help in setting up calculations. This
> >>>> >> tutorial
> >>>> >> is for NAMD 2.6 but the system setup process should be the same as
> >>>> >> NAMD2.7b1.
> >>>> >>
> >>>> >> NAMD2.6 FEP tutorial:
> >>>> >>
> >>>> >>
> http://www.ks.uiuc.edu/Research/namd/tutorial/fep/AlchemicalFEP-Mar2008.pdf
> >>>> >>
> >>>> >> Required files for tutorial:
> >>>> >>
> >>>> >>
> >>>> >>
> http://www.ks.uiuc.edu/Research/namd/tutorial/fep/AlchemicalFEP-Mar2008.zip
> >>>> >>
> >>>> >>
> >>>> >> 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 Voice: 217-244-1733
> >>>> >> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >> On Mon, May 4, 2009 at 2:54 PM, yun luo <luoyun724_at_gmail.com>
> wrote:
> >>>> >>>
> >>>> >>> Hi,
> >>>> >>>
> >>>> >>> I'm using NAMD2.7 for running FEP. I need to disappear a sodium
> ion
> >>>> >>> in my
> >>>> >>> membrane. So I overlay a dummy atom with 0 mass 0 charge 0 radius
> on
> >>>> >>> a
> >>>> >>> sodium ion. But I got a warning below:
> >>>> >>>
> >>>> >>> Warning: FOUND 1 ATOMS WITH ZERO OR NEGATIVE MASSES! CHANGED TO
> >>>> >>> 0.001
> >>>> >>>
> >>>> >>> I'm wondering if the nonzero mass will effect the energy? If yes,
> >>>> >>> how to
> >>>> >>> stop this automatic changing?
> >>>> >>>
> >>>> >>> Thanks!
> >>>> >>>
> >>>> >>> Ly
> >>>> >>
> >>>> >
> >>>> >
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> saludos desde el fin del mundo
> >>
> >
> >
> >
> > --
> > saludos desde el fin del mundo
> >
>
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