From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Sat May 01 2010 - 08:03:01 CDT
Dear Axel,
Execuse me for my late reply!
Thanks a lot for you suggestion.
>ok. the difficulty is that i don't know your code and i know from personal
>experience, how easy it is to miss a factor of two or similar somewhere.
If you are interested in my code, i would glad to show you the part of calculating the total electrostatic energy.
>i am not so sure about "same structure"
I'm sorry for my poor description in english. More detailed, it is to say i download a X-ray or NMR protein 3D structure and calculate the electrostatic energy of the structure respectively with my code and NAMD.
>i am not so sure about "same structure". you mention minimization, you
>also mentioned polarizability at some point. are you _really_ comparing
>apples to apples here?
Yes, I like apples! The reason i mentioned polarizabiltiy is that I just tried to explain, in my opinion, that whether different dielectric constant be used.
Hopefully, i feed you curiosity.
Conversely, Will you please briefly explain how namd get the electrostatic energy of a system, so that i can see what's wrong with my code. Are you okay?
Appreciate your time very much!!
All the best,
Yandong,
在2010-04-30 10:34:42,"Axel Kohlmeyer" <akohlmey_at_gmail.com> 写道:
>On Thu, Apr 29, 2010 at 9:59 PM, ydhuang2727 <ydhuang2727_at_163.com> wrote:
>> Dear Axel,
>> Well, let me put others aside, and what i'm comparing is the
>> electrostatic energy obtain by my code and by namd with the same force
>> field.
>
>ok. the difficulty is that i don't know your code and i know from personal
>experience, how easy it is to miss a factor of two or similar somewhere.
>
>> And my problem is why they are so different for the same structure.
>
>i am not so sure about "same structure". you mention minimization, you
>also mentioned polarizability at some point. are you _really_ comparing
>apples to apples here? i would only compare energies at the zeroth
>step when you feed NAMD and your code the _exact_ same coordinates,
>the same box size etc. then and only then each of the components should
>be the same. minimization in a highly dimensional coordinate system,
>can very easily lead to different minima.
>
>just setting the dielectric constant to a different value
>
>> My Simulation goes well and reach equilibrium, energy constant, in
>> NVE ensemble. But i still feel worried about such a clear and unreasonable
>> difference when dielectric constant is 1.0.
>
>well, have you tried some much simpler systems?
>like two water molecules without periodic boundaries?
>where you can compute and compare energies and forces
>even with a pencil and a piece of paper?
>
>a simulation that runs and conserves energy proves that
>your integrator is correct and that your time step, you cutoff
>and other parameters are reasonable, but it does not at all
>prove that your interactions are computed correctly. i have
>had this happen to me just about a year ago.
>
>> In other words, I think the so-called "set velocity zero" is somewhat
>> like damped MD as you mentioned. And my approachment is simply and crudely
>> make the velocity damped directly down to zero but with a relax time.
>
>ok. the "relax time" part is what was missing and what was tickling
>my curiosity. thanks a lot for providing this information. it may occasionally
>come over as a bit rough, but one of the major forms of "payback"
>that one can get from answering questions on mailing lists is that
>people satisfy somebody's curiosity. so i always feel like being
>cheated out of my share, if other people get their questions answered,
>come back with more questions, but don't answer mine.
>
>cheers,
> axel.
>
>
>> Thanks for your time!
>>
>> Best wishes,
>>
>> Yandong,
>>
>> 在2010-04-29 21:34:36,"Axel Kohlmeyer" <akohlmey_at_gmail.com> 写道:
>>>On Thu, Apr 29, 2010 at 8:39 AM, ydhuang2727 <ydhuang2727_at_163.com> wrote:
>>>> Dear Jerome,
>>>>
>>>> Thanks for your kind analysis.
>>>> The dielectric constant of a protein is about 2 to 4, thus when the protein
>>>> is polarizable, a proper dielectric constant bigger than 1.0 should be
>>>> adopted to reduce the intensity bwteen two charged atoms. Should we?
>>>
>>>no. why?? the dielectric constant is a _result_ of the charges in your system
>>>reacting to its environment. if you use explicit charges, your
>>>dielectric constant
>>>should _always_ be 1.0. setting it to a larger value is a (crude) approximation
>>>to an implicit solvent. in this case you (wrongly) would assume a continuum
>>>solvent. but inside a protein you are making a large error, since you would
>>>not have any solvent there.
>>>
>>>> If this is the case, i can abtain the same values as what namd got.
>>>
>>>perhaps you should _first_ explain to us what you are actually comparing.
>>>it looks to me as if you are doing an apples to oranges comparison and
>>>trying to fix up stuff with an empirical scaling factor is not going
>>>to help much.
>>>
>>>also, you still owe us an explanation for how your atoms can move when
>>>you set the velocities to zero.
>>>
>>>thanks,
>>> axel.
>>>
>>>
>>>> Appreciate your attention!
>>>>
>>>>
>>>> Good day!
>>>>
>>>> Yandong,
>>>>
>>>>
>>>> 在2010-04-29 15:59:42,"Jérôme Hénin" <jhenin_at_ifr88.cnrs-mrs.fr> 写道:
>>>>>Dear Yangdong,
>>>>>
>>>>>> Based on the CHARMM22 force field, i use my own code to roughly minimize
>>>>>> a peptide and compare each term of interactions with the results of
>>>>>> minimization of namd2.6. My approachment is simply to set velocity zero
>>>>>> everay step, which is inferior to annealing algorithm that namd may adpot.
>>>>>>
>>>>>> All interactions are comparable and consistent with the results of namd
>>>>>> except for electrostatic interaction when dielectric constant is 1.0, the
>>>>>> absolute value of which by my code is nearly twice as big as that by namd.
>>>>>> As to VDW and Electrostatic interactions, all pairs of atoms without bond
>>>>>> interaction( bond stress, angle bend, dihedral torsion, improper dihedral)
>>>>>> are considered in my code. I did not use cut-off method. Can you find
>>>>>> something wrong?
>>>>>
>>>>>Maybe. In the CHARMM ff, the rule is to include nonbonded terms for
>>>>>all atoms except those linked through one or two bonds (which will
>>>>>typically be coupled by bond and angle terms). Atoms connected by a
>>>>>torsion term (3 bonds) have their full nonbonded interactions (the
>>>>>so-called 1,4-interactions). There are a few exceptions: for some atom
>>>>>types, the CHARMM parameter files list modified Lennard-Jones
>>>>>parameters for 1,4 interactions. Electrostatics is never modified,
>>>>>though.
>>>>>
>>>>>Cheers,
>>>>>Jerome
>>>>
>>>>
>>>> ________________________________
>>>> 网易为中小企业免费提供企业邮箱(自主域名)
>>>
>>>
>>>
>>>--
>>>Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>>>http://sites.google.com/site/akohlmey/
>>>
>>>Institute for Computational Molecular Science
>>>Temple University, Philadelphia PA, USA.
>>>
>>
>>
>> ________________________________
>> 网易为中小企业免费提供企业邮箱(自主域名)
>
>
>
>--
>Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>http://sites.google.com/site/akohlmey/
>
>Institute for Computational Molecular Science
>Temple University, Philadelphia PA, USA.
>
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