From: yun luo (luoyun724_at_gmail.com)
Date: Wed May 06 2009 - 11:50:06 CDT
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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