From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 29 2010 - 21:34:42 CDT
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
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.
> Thanks for your time!
> Best wishes,
> 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
>>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.
>>> Appreciate your attention!
>>> Good day!
>>> 在2010-04-29 15:59:42，"Jérôme Hénin" <jhenin_at_ifr88.cnrs-mrs.fr> 写道：
>>>>> 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,
>>Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>>Institute for Computational Molecular Science
>>Temple University, Philadelphia PA, USA.
-- 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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