Re:Re: Re: Dielectric Constant

From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Thu Apr 29 2010 - 01:19:46 CDT

Dear Axel,
Thanks for your suggestion!
 
Best,
 
Yandong,

在2010-04-29 13:06:18,"Axel Kohlmeyer" <akohlmey_at_gmail.com> 写道:
>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,
>>>>>
>>>>> ________________________________
>>>>> 网易免费域名邮箱正式上线
>>>>
>>>>
>>>>
>>>>--
>>>>Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>>>>http://sites.google.com/site/akohlmey/
>>>>
>>>>Institute for Computational Molecular Science
>>>>Temple University, Philadelphia PA, USA.
>>>>
>>>
>>>
>>> ________________________________
>>> 网易为中小企业免费提供企业邮箱(自主域名)
>>
>>
>>
>> --
>> 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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