Hi Catherine,
To add some more practical advice to this discussion. In a slight rephrasing
of what Thomas says I would state that your simulations need to be long
enough that the property you are attempting to measure is not dependent on
the length of the simulation. This is another way of saying that your
simulation is converged. I would start by going back over what you learnt as
an undergrad for statistical error analysis. Most people learn this in terms
of experiment but the same principles apply to MD computer simulation and it
can be helpful to think of the simulations in terms of experiment.
A simple test and one I recommend is to calculate the property you are
interested in based on the data you have, then double the run length and see
if the property changes and if so by how much. This will at least give you
some idea of the sampling error due to convergence and will give you
ammunition to defend the length of your simulations. Another way to do this
is to effectively throw away half your data. Take just the first half of
your data and calculate the properties you are interested in, say a binding
energy. Then repeat that with just the second half of the data, then repeat
it with all the data and compare the results. You can also take this one
step further and script it such that you show convergence of the property
being measured as a function of your dataset size. This is pretty easy to do
and something I think everyone publishing such things should do. However, I
suspect that in most cases things are horribly unconverged and so showing
such a plot would 'detract' from the result a little too much. It is nice to
do though just to prove to yourself if the data is converged or not. Take a
MMPBSA calculation for example. Say you have 10,000 frames. Write a simple
script that starts with the data for frame 1 and calculates the binding
energy, then repeats this for frames 1,2 combined, then 1,2,3, then 1 to 4
etc. If you convert the frames into time, as in frame 1 = 10ps, frame 2 =
20ps etc you can then easily plot the binding energy as a function of
cumulative simulation time. This function 'SHOULD' converge since each point
includes all the previous points. You'll be shocked though how long it
actually takes to converge. However, armed with such data showing
convergence I think you can easily convince a skeptical reviewer that your
simulation lengths (and number of simulations) were sufficient.
Good luck,
All the best
Ross
> -----Original Message-----
> From: steinbrt.rci.rutgers.edu [mailto:steinbrt.rci.rutgers.edu]
> Sent: Friday, July 06, 2012 2:51 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] What is the typical stimulation time?
>
> Hi,
>
> well, there have been many responses so far, some of them serious...
>
> Still, to give my two cents: You should rephrase the question into a
> statement. When you write up your manuscript, think about adding that
> you
> are confident that the results presented from a simulation of length X
> are
> sufficiently converged, because...
>
> ...and then it depends on what you want to say, e.g. because multiple
> transitions along a reaction coordinate that you study have been
> observed,
> because the correlation time of whatever property you look at is much
> smaller than X, because you get good agreement to experiment, etc. The
> last one may not be such a good justification, but is seen in papers
> often
> enough.
>
> Kind Regards,,
>
> Thomas
>
>
> On Thu, July 5, 2012 10:25 pm, Dr. Vitaly V. G. Chaban wrote:
> > and whether the simulation is equilibrium dynamics, but we go
> flooding...
> >
> > Good journals do not like to accept applicable simulation studies
> > based on less than 10 ns trajectories, this is a purely practical
> > advice/observation.
> >
> > Vitaly
> >
> >
> > On Thu, Jul 5, 2012 at 10:06 PM, Ganesh Kamath
> <gkamath9173.gmail.com>
> > wrote:
> >> Depends on what you are trying to simulate ......
> >>
> >> On Jul 5, 2012 8:56 PM, "Dr. Vitaly V. G. Chaban"
> <vvchaban.gmail.com>
> >> wrote:
> >>>
> >>> >
> >>> > Dear Sir/Madam,
> >>> > What is the typical simulation time to get a reasonable and data
> for
> >>> > publications use?
> >>> > Best regards,
> >>> > Catherine
> >>>
> >>> Catherine -
> >>>
> >>> Not any femtosecond more after ergodicity is achieved.
> >>>
> >>>
> >>> Dr. Vitaly V. Chaban, 430 Hutchison Hall
> >>> Dept. Chemistry, University of Rochester
> >>> 120 Trustee Road, Rochester, NY 14627-0216
> >>> THE UNITED STATES OF AMERICA
> >>>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
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Received on Fri Jul 06 2012 - 09:30:03 PDT
