Re: dummy atom mass changed

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Wed May 06 2009 - 13:09:26 CDT

Ly,

Decouple controls the number of additional PME grids calculated during a
FEP.

1. How large is your water box and what is your cutoff?

2. How far is the ion from it's recipricol image? Off the cuff (ie wild
guess) I wonder if your ion is experiencing an interaction with its
recipricol image that's being scaled when decouple is off vs. not being
scaled when decouple is on.

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 Wed, May 6, 2009 at 11:50 AM, yun luo <luoyun724_at_gmail.com> wrote:
> Could anybody explain me what the "decouple on" do in case of disappearing
> one ion in pure water ?
>
> On Tue, May 5, 2009 at 3:26 PM, yun luo <luoyun724_at_gmail.com> wrote:
>
>> Hi Christ,
>>
>> Thanks for your notice. According to the ug, "decouple" is dealing with
>> intramolecular interactions. Since I only disappear one ion, there is no
>> intramolecular interaction. So I think decouple on/off should give similar
>> result. However, I disappear one sodium ion in TIP3 box with:
>>
>> fepVdwLambdaEnd 1.0
>> fepElecLambdaStart 0.5
>> fepVdwShiftCoeff 5.0
>> decouple on/off
>>
>> I got dG=-73 kcal/mol with "decouple on" and dG=-89 kcal/mol with
>> "decouple off (default)". How do you think those value? Where does the
>> difference come from?
>>
>>
>> On Tue, May 5, 2009 at 12:53 PM, Chris Harrison <char_at_ks.uiuc.edu> wrote:
>>
>>> 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 <http://www.ks.uiuc.edu/%7Echar>
>>>     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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