Hi,
Just to add to what Jason said, just to even properly populate your
mass-weighted covariance matrix you will need at least as many frames
as you have rows (i.e. N = # atoms in your covariance matrix times 3).
For a good estimate of the entropy I suspect you'll probably want at
least 10 times that, although I'm sure some of the articles Jason
pointed out have better recommendations. One measure you can use is to
perform your quasi-harmonic calculation, then extend your simulations
by N frames and observe how your calculated values change.
-Dan
On Thu, Feb 11, 2016 at 9:42 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Feb 11, 2016 at 10:34 AM, Aronica, Pietro <
> pietro.aronica07.imperial.ac.uk> wrote:
>
>> Hello,
>> I wanted to perform quasi-harmonic calculations of an interaction I have
>> to estimate the entropy. I have been told that in order for this to work
>> properly, the simulation needs to be of at least a certain length. I've
>> also been told that this issue had been discussed on the mailing list
>> before, but I have failed to find relevant information, just hints, and the
>> tutorials are rather vague on the subject. Where can I find exact
>> information on how quasi-harmonic calculations ought to be run?
>>
>
> Journal articles. There seem to be some promising hits on Google Scholar:
> https://scholar.google.com/scholar?hl=en&q=quasi-harmonic+entropy&btnG=&as_sdt=1%2C5&as_sdtp=
>
> It may also take some amount of "try it and see" (e.g., in terms of how
> many frames to include, etc.).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Thu Feb 11 2016 - 09:30:03 PST
