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 -- View this message in context: http://gromacs.5086.x6.nabble.com/local-pressure-tp5007803p5007844.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
