From: yun luo (luoyun724_at_gmail.com)
Date: Tue May 05 2009 - 15:26:46 CDT
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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