See the supporting info in this publication:
http://pubs.acs.org/doi/abs/10.1021/jp4125099
-Dan
On Fri, Jun 20, 2014 at 8:25 AM, James Starlight <jmsstarlight.gmail.com>
wrote:
> One question about possible algorithm for quick checking of the convergence
> of my trajectory (ies).
> For instance I'd like to write some simple script having as the input
> several trajectories of the same system with different length to check (for
> instance by means of principal mode analysis or another not very expensive
> method) in what case my system have been converged fully. Are there any
> examples of such scripts or ready workflows?
>
> James
>
>
> 2014-06-19 17:52 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
>
> > Thanks, Jason!
> >
> > It's very useful advises and you've made very great script library! I'll
> > try to follow your basic ideas during my own studies.
> >
> > James
> >
> >
> > 2014-06-17 23:25 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> >
> > On Tue, 2014-06-17 at 22:16 +0400, James Starlight wrote:
> >> > Hi Dan,
> >> >
> >> >
> >> > many thanks for the bash guide- I've found it very useful. In general
> >> I'd
> >> > like to look at some basic bash script examples suitable for typical
> md
> >> > jobs dealing with the running of many of simulation on clusters
> because
> >> the
> >> > most complicated examples like replica exchange simulation have
> already
> >> > been present in the amber tutorials.
> >>
> >> You've gotten the most helpful responses you can possibly get about your
> >> question so far, so I won't belabor the points others have made. I'll
> >> relay my own opinions on the topic, though.
> >>
> >> Scripting is, at its core, simply a tool we (as computational
> >> scientists) use to increase our efficiency and productivity. For
> >> example, high-throughput work like screening a database of millions of
> >> compounds cannot be done unless "scripted."
> >>
> >> When you are designing an experiment or calculation you want to perform,
> >> you have a list of tasks you need to get done. Designing a script to
> >> carry out these tasks requires you to divide your problem up into
> >> simpler chunks that can be easily represented with common logic
> >> structures in programming/scripting, like loops and simple conditionals.
> >> Writing the script is easy -- if you don't know the syntax of doing
> >> something like looping over a list, you can google your question and see
> >> that it has most likely been asked and answered several times on
> >> StackOverflow before.
> >>
> >> _Designing_ the script is the real challenge (it is an art). It is not
> >> something easily taught in a tutorial (nor is there any one "right" way
> >> to do it). You can use the existing tutorials, and the scripts written
> >> therein, to try and reverse-engineer the design and try to understand
> >> the thought process that led the tutorial authors to write it that way.
> >> Then if you're ambitious, try improving it.
> >>
> >> When you are doing your own project, focus on carrying out your
> >> experiment. If you come up to a part that is particularly repetitive or
> >> something that fits conceptually into a scripting or programming
> >> paradigm, write a script to handle that part (Googling your question
> >> when you don't know how to do something). The more you do this, the
> >> better you will get at scripting and the more you will be able to
> >> automate your workflows.
> >>
> >> If you find yourself doing the same thing over and over for different
> >> projects (like imaging a trajectory or RMS-fitting your system with
> >> cpptraj or computing a distance and plotting the result), try to write a
> >> script to automate that task. As your experience in the field grows, so
> >> too will your library of scripts you find useful and your scripting
> >> ability overall. Mine is here: https://github.com/swails/jmsscripts/
> and
> >> a trained eye can clearly see which ones I wrote when I was experienced
> >> and which I didn't.
> >>
> >> 6 years ago, I had never used Unix before. I was decent at scripting
> >> within a few months and quite strong within a year or two -- all
> >> following the above advice. That which is self-learned is learned the
> >> best (and is remembered the longest).
> >>
> >> Always rambling,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Fri Jun 20 2014 - 08:00:03 PDT
