**From:** yun luo (*luoyun724_at_gmail.com*)

**Date:** Wed May 06 2009 - 11:50:06 CDT

**Next message:**Roman Petrenko: "Re: diffusion / fex peptide problem"**Previous message:**Anton Arkhipov: "Re: Langevin damping coefficient"**In reply to:**yun luo: "Re: dummy atom mass changed"**Next in thread:**Chris Harrison: "Re: dummy atom mass changed"**Reply:**Chris Harrison: "Re: dummy atom mass changed"**Reply:**Floris Buelens: "Re: dummy atom mass changed"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
*

*>>>> >
*

*>>>>
*

*>>>
*

*>>>
*

*>>
*

*>
*

**Next message:**Roman Petrenko: "Re: diffusion / fex peptide problem"**Previous message:**Anton Arkhipov: "Re: Langevin damping coefficient"**In reply to:**yun luo: "Re: dummy atom mass changed"**Next in thread:**Chris Harrison: "Re: dummy atom mass changed"**Reply:**Chris Harrison: "Re: dummy atom mass changed"**Reply:**Floris Buelens: "Re: dummy atom mass changed"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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