AMBER Archive (2009)

Subject: Re: [AMBER] Can I get an average trajectory?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Nov 18 2009 - 06:08:59 CST

i'm not sure how you would do this, but I don't think it's really what you
want. averaging over trajectories that are different will probably give you
unphysical structures. what you normally want to do is average the analysis
data, not the structures.
if you want to "eliminate stochastic properties", why not average over a
period of time in your trajectory and see if it looks like what you want?
this will help decide if it's worth the effort to average over multiple
trajectories.

On Tue, Nov 17, 2009 at 11:46 PM, cyk5056 <cyk5056_at_163.com> wrote:

> Hi Amber users,
> I am doing MD and have obtained several binary trajectory files. To
> eliminate the stochastic properties, I want to average these trajectory(all
> 0-500ps) into one 0-500ps trajectory. How can I do that? I think maybe it is
> not easy to average them in binary form. Maybe I can use Matlab to average
> them if they are in ascii form. So how to convert them into ascii form?
> Either of these two approaches will work, I think.
> BTW: I have tried "average" instruction and it will return a average
> structure, not a trajectory
>
> Thank you very much!
>
>
> Best,
>
>
>
>
>
> cyk5056
> 2009-11-18
>
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