Re: dummy atom mass changed

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Tue May 05 2009 - 12:53:00 CDT

Ly,

The code has been changing very quickly in the last several months and the
default values for your softcore parameters will depend on when you checked
out the cvs or downloaded the beta. I very strongly say this: set the
parameters yourself. Until beta2, do not assume the softcore parameters'
default values. Until beta2, do not assume the softcore parameters' default
values in the users guide are correct. Because the code has been changing
so rapidly, SET THE SOFTCORE PARAMETERS MANUALLY based on the below
suggestion.

The default values in the cvs are currently, and will be in NAMD2.7b2:

fepVdwLambdaEnd = 1.0
fepElecLambdaStart=0.5
fepVdwShiftCoeff=5.0

If you want to use softcore in an FEP you should probably start with the
following parameters and values:

fepVdwLambdaEnd 1.0
fepElecLambdaStart 0.5
fepVdwShiftCoeff 5.0
decouple on

MAKE SURE to set decouple to on. It's default, for other reasons, is
currently set to off.

Thanks for your feedback. It is valuable input as we try to resolve any
problems during the beta phase

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               Fax: 217-244-6078
On Tue, May 5, 2009 at 11:49 AM, yun luo <luoyun724_at_gmail.com> wrote:
> 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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