From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Thu Apr 29 2010 - 20:59:23 CDT
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.
And my problem is why they are so different for the same structure.
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.
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.
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
>>
>>
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>
>
>
>--
>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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