Re: Re: Dielectric Constant

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 29 2010 - 00:06:18 CDT

2010/4/29 Axel Kohlmeyer <akohlmey_at_gmail.com>:
> 2010/4/28 ydhuang2727 <ydhuang2727_at_163.com>:
>> Dear Axel,
>>
>> Thanks.
>> Well, here comes another question more detailed, that:
>>
>> 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.

on top of that. how can anything move in your system, when you set
the velocity to 0.0 in _every_ step? that doesn't make any sense.

...and adding damped dynamics, which is much more effective than
annealing, is only a few additional lines, if you have your own code.

a.

>> 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?
>
> sorry, but asking me to debug _your_ code is asking a *lot*.
>
> how should i know what you programmed???
>
> a.
>
>> Thanks for your time!
>>
>> Good day,
>>
>> Yandong,
>>
>> 在2010-04-29 00:17:58,"Axel Kohlmeyer" <akohlmey_at_gmail.com> 写道:
>>>2010/4/27 ydhuang2727 <ydhuang2727_at_163.com>:
>>>> Dear NAMD developers,
>>>>
>>>> Will you please tell me what the dielectric constant NAMD uses in the
>>>> Comlombic potential, when i simulate a protein in vacuum. Is it still 1.0?
>>>
>>>yes. why should it be any different?
>>>
>>>an MD code like NAMD doesn't really know what kind of system
>>>you feed it. all it sees is positions and interactions between them.
>>>
>>>cheers,
>>> axel.
>>>
>>>
>>>>
>>>>
>>>> Best wishes!
>>>>
>>>>
>>>> Yandong,
>>>>
>>>> ________________________________
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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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>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> 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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