From: daniel aguayo (bioquimico_at_gmail.com)
Date: Mon May 04 2009 - 19:53:14 CDT
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
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