Re: dummy atom mass changed

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue May 05 2009 - 10:43:48 CDT

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               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               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
>


lambda.png

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