[gmx-users] Re: local pressure

[ohsOllila]

Hi everybody,

There is some more information about the issue in the MARTINI web page: 
http://md.chem.rug.nl/cgmartini/index.php/3d

>From there you can download the tools to analyze the binary file
localpressure.dat which is given out by a gromacs code. There is more
information in the README file in the pressure-tools package and also in the
publications [1,2,3,4].

I have tested the version linked in the MARTINI page pretty widely against
independently written code and the results are the same, thus I think it is
pretty reliable. I know that there exist also a version for 4.5. since some
people have asked me about the results they have calculated with that. Based
on those discussions I have got an impression that the version for 4.5.
gives different results than the version linked in the MARTINI page.
However, I have not tested the version for 4.5. myself and I do not have it.

I do get questions related to the pressure profile calculations monthly and
the paper reperesenting the methos for 3D calculations [1] also gets
regularly cited (44 total, 13 this year) so I think that there is some
interest on this issue. Also several people have been able to perform these
calculations so it is doable. Since the code is ment to work as rerun
analysis, one can split the trajectory in the pieces and separately analyze
them (trivial parallelization). This helps if the code is too slow.


[1] Ollila et al. PRL 102: 078101 (2009)
[2] Ollila et al. Biophysical Journal, Volume 100, Issue 7, 1651-1659 (2011)
[3] Ollila et al. Biophysical Journal, Volume 103, Issue 6, 1236-1244 (2012)
[4] Ollila PHD thesis, http://dspace.cc.tut.fi/dpub/handle/123456789/6813

BR,
Samuli Ollila



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