Re: dummy atom mass changed

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Mon May 04 2009 - 22:24:32 CDT

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
>

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