From: JťrŰme Hťnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Apr 29 2010 - 10:06:57 CDT
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.
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.
> ¬† ¬†axel.
>> Appreciate your attention!
>> Good day!
> Dr. Axel Kohlmeyer ¬† ¬†akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
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