Re: Can DCD trajectory files contain only protein but water surround

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 13 2011 - 19:57:05 CST

2011/1/13 yandong Huang <ydhuang2727_at_163.com>:
> Dear all,
>
> Usually, DCD trajectory files contain the whole system including water.
>
> In my case, i need to save each step the coordination as well as velocity of
> my protein. So it's not suitable to set a bigger DCDfreq value, which
> is suggested to reduce DCD file size.

if you need that kind of information this often (why?), wouldn't it be better
to include the computation that you want to do into the simulation?

with such frequent i/o and writing velocities to boot, you seriously
increase the serial part of the code and thus limit the performance.
doing the computation (i am curious which one, btw) on-the-fly
would be much more efficient.

> You know, water takes a big part of the computational system. Therefore, if
> the DCD contains only protein, the DCD trajectory file would not be so big.
> But how to realize it?

this can be done in post processing, but you might also consider
using an alternate MD code that has more flexible output option
(at the expense of computational efficiency).

cheers,
    axel.

> I have checked the user guider of NAMD, but get no result.
>
> Thanks in advance!
>
>
> Good day,
>
> Yandong,
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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