# Re: [AMBER] How to get average from 3 repeated tracjectory

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thu, 13 Oct 2016 11:16:00 -0400

presenting the time course of data that is averaged across 3 runs probably
would not be meaningful. if you want to calculate an average across all 3
runs, you could average data from each, then average the 3 results, or you
can just concatenate the 3 trajectory files in cpptraj and get your data
from that. it still will not be meaningful if you plot it as time dependent
data though. you should think about exactly what you are trying to extract,
and how to do the averaging in a way that makes sense. we can tell you how
to carry out certain data analysis, but you need to think about what you
want your data to show. most often, you will want to draw conclusions from
one of your trajectories, and then use the others as a way to determine how
reliable those conclusions are. sometimes multiple trajectories are used to
gain statistics on timescales of rare events.

you can do what you propose, but it may or may not be useful depending on
what you are trying to average and what you want to learn.

On Thu, Oct 13, 2016 at 11:08 AM, Setyanto Md <stwahyudi.md.gmail.com>
wrote:

> Hi Hai,
>
> I just want to make it simple. Usually I have to analysis rmsd, rmsf, etc
> from three (3) trajectory (the result from three simulation).
>
> Can we just analysis rmsd, rmsf, etc from one (1) trajectory, which is an
> average from three (3) trajectory. ?
>
> Thanks
>
> Setyanto
>
> On Thu, Oct 13, 2016 at 10:00 PM, Nhai <nhai.qn.gmail.com> wrote:
>
> > Hi
> >
> > What do you want to learn from you that kind of averaging?
> >
> > Hai
> >
> > > On Oct 13, 2016, at 10:50 AM, Setyanto Md <stwahyudi.md.gmail.com>
> > wrote:
> > >
> > > Dear Amber User and Developer,
> > >
> > > I just run 3 simulation from 3 different initial structure.
> > > Then i get 3 trajectory.
> > >
> > > Instead of make analysis from each trajectory, I'd like to get a single
> > > trajectory average from 3 trajectory.
> > >
> > > Is there any example command in cpptraj to get trajectory average from
> 3
> > > different trajectory. ?
> > >
> > > Thank you
> > >
> > > Setyanto TW
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Received on Thu Oct 13 2016 - 08:30:03 PDT
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