Re: Re: Re: Dielectric Constant

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 29 2010 - 08:34:36 CDT

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.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:03 CST