Re: Characteristic time of atomic vibrations and collisions?

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Tue Jan 15 2008 - 10:06:29 CST

Victor,

Thanks for your reply. As I have found out, the atomic motions we want
to simulate with MD have a spectrum of timescales, notably ranging from
10^(-14) to 10^(-12) seconds. The fast vibrations of covalently bonded
H atoms have periods from 9 to 10 fs and the MD timestep needs to be
smaller.

Long

Quoting Victor Ovchinnikov <ovchinnv_at_MIT.EDU>:

> Long,
> You need to consider bond stretching frequencies, which will be of the
> order of 2000 cm-1; this corresponds roughly to 17 fs per period.
> Victor
>
> On Mon, 2008-01-14 at 17:16 -0500, Yinglong Miao wrote:
>> Dear NAMD users,
>>
>> Here I have a quite fundamental question generally for MD. 1fs is the
>> typical MD timestep we have been using for MD simulations. But as I
>> searched for information about characteristic time of atomic vibrations
>> and collisions, I found 10^12 for the atomic vibration frequency on one
>> of the websites. This should indicate the characteristic time as
>> 10^(-12) s, which is 10^3 times larger than our MD timestep. It's right
>> that the MD timestep needs to be smaller than the fastest vibrational
>> frequency in the system, but how can this gap be so big? Or the number
>> I found is not correct in some sense?
>>
>> Thanks,
>> Long
>>
>> --
>> Yinglong Miao
>> Ph.D. Candidate
>> Center for Cell and Virus Theory
>> Chemistry Department, Indiana University
>> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
>> Tel: 1-812-856-0981
>>
>
>

--
Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981

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