Re: dummy atom mass changed

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Tue May 05 2009 - 10:18:39 CDT

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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