From: yun luo (luoyun724_at_gmail.com)
Date: Tue May 12 2009 - 11:10:11 CDT
Hello,
I keep the fepVdwLambdaEnd=1.0, but change the fepElecLambdaStart from 0.2
to 0.8 with decouple on. The energy of disappearing an ion in bulk water
shift a lot. Are the different fepElecLambdaStart value supposed to only
change the path but total enegry should converge at the end?
On Thu, May 7, 2009 at 11:18 AM, yun luo <luoyun724_at_gmail.com> wrote:
> Thank you, Christ and Floris, that makes sense. I used the same system as
> the "Charging a spherical ion" example for NAMD2.6. The ion is growing in a
> box with length of 30 A and I use "switchdist 10 cutoff 12". The ion is
> fixed in the center of box. So it's 30 A away from it's image. I will test a
> larger box to see if I get the similar solvation energy.
>
> Lyna
>
>
>
> On Thu, May 7, 2009 at 5:09 AM, Floris Buelens <floris_buelens_at_yahoo.com>wrote:
>
>>
>> Hi, I can confirm what Chris said - it's clear why you'd assume that
>> 'decouple on' shouldn't affect a single-atom perturbation but there is a
>> difference arising from PME. With 'decouple off' the end state is an atom
>> with no non-bonded interactions whatsoever (vdW or electrostatic), while
>> with 'decouple on' non-bonded interactions across the periodic boundary are
>> still in effect; vdW interactions will be beyond the cutoff but a charged
>> atom will still interact with its periodic images.
>> best regards,
>>
>> Floris
>>
>> ________________________________
>> From: yun luo <luoyun724_at_gmail.com>
>> To: char_at_ks.uiuc.edu
>> Cc: NAMD <namd-l_at_ks.uiuc.edu>
>> Sent: Wednesday, 6 May, 2009 17:50:06
>> Subject: Re: namd-l: dummy atom mass changed
>>
>> 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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