From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Apr 28 2010 - 23:44:20 CDT
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.
>
> 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.
>>
>
>
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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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