[gmx-users] Obtain frames from every one ps

[Justin Lemkul]

On Tue, Apr 9, 2013 at 2:13 AM, Ashalatha Sreshty <sreshtyphd at gmail.com>wrote:

> Dear All,
>
> I need help in obtaining frames from every one ps of a trajectory. My
> problem is as described:
>
> I obtained a 100ns trajectory, I get one frame for every 5 ps from my
> initial, but my new trajectory is generated by catenating different frames
> that fall in the bins of PCA space of the first two PC components with
> lowest energy. Now that, I want to do the analysis like angle average, RMSD
> etc on all the frames, I would like to know how to obtain frames from this
> new trajectory at every one ps.
>
>
If you're binning structures that were produced every 5 ps, there's no way
to say that they occurred every 1 ps. Moreover, isn't time rather
irrelevant if you've binned structures that may not be continuous in time,
anyway? You can assign whatever frame interval you like with trjconv
-timestep, but whether or not doing so makes any sense is up to you to
decide.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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