Thank you for the suggestion.
On Thu, Oct 13, 2016 at 10:16 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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.
>
> so overall there is not a good answer to your question. the answer is yes
> 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 - 16:30:02 PDT
