Re: Re: Re: Dielectric Constant

From: JťrŰme Hťnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Apr 29 2010 - 10:06:57 CDT

Hey Axel,

I don't mind doing the good cop, bad cop spiel once in a while, but
here I think you've drifted to the Robocop side. Next thing we know
you'll be in full Terminator mode.

Of course you're right about the energy comparison, that sounded very
unclear. But you could get over the velocity quenching thing, which
was just a matter of unfortunate wording, about 4 posts back. There's
enough to sort out without bringing that back up.

Cheers,
Jerome

On 29 April 2010 15:34, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 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,
>>
>>
>> Śú®2010-04-29¬†15:59:42ÔľĆ"J√©r√īme¬†H√©nin"¬†<jhenin_at_ifr88.cnrs-mrs.fr>¬†ŚÜôťĀďÔľö
>>>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
>>
>>
>> ________________________________
>> ÁĹĎśėďšłļšł≠ŚįŹšľĀšłöŚÖćŤīĻśŹźšĺõšľĀšłöťāģÁģĪÔľąŤá™šłĽŚüüŚźćÔľČ
>
>
>
> --
> 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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