Ok, I did rerun with local pressure mdrun, and got pressure.dat* files in binary format. how do I proceed from here? Any utility to analyze or post-process this?
On Wed, May 1, 2013 at 11:11 AM, Sikandar Mashayak <symasha...@gmail.com>wrote: > Thanks Xavier, > > I will give it a try. > > > On Wed, May 1, 2013 at 10:56 AM, XAvier Periole <x.peri...@rug.nl> wrote: > >> >> >> Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E. Lindahl are >> :)). >> >> The paper related to the use would be: >> Ollila et al, PRL 102, 078101 (2009) >> Ollila et al, Biophysical Journal (100)1651–59 >> >> On May 1, 2013, at 5:48 PM, Sikandar Mashayak <symasha...@gmail.com> >> wrote: >> >> > Thanks Xavier >> > >> > >> > Can you please elaborate on how to use and post-process the local >> pressure >> > version of gromacs? Do you have any examples or reference article? >> > >> > May be you can create a HowTo wiki as Justin suggested, it would be of >> > great help. >> > >> > Thanks >> > Sikandar >> > >> > >> > On Wed, May 1, 2013 at 5:03 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> > >> >> >> >> >> >> On 5/1/13 5:12 AM, XAvier Periole wrote: >> >> >> >>> >> >>> The use of the original code is quite straightforward, the post >> >>> processing is a bit more confusing but quite accessible. >> >>> >> >>> >> >> That would be a great topic for a wiki How-To. >> >> >> >> >> >> We have been using this code (the one available on the site) and >> related >> >>> version in the lab and we definitely would find it very sad to not >> keep >> >>> this feature available in GROMACS. >> >>> >> >>> >> >> I never said it would go away, but given the fact that there have been >> no >> >> updates to the git branch in over 3 years, it's simply unlikely that >> anyone >> >> has cared to move it forward. If someone wants to update the code to >> be >> >> compatible with 4.6, that would be a welcome contribution. Lack of any >> >> request for improvements and inclusion in an official release has >> likely >> >> led to the decline in interest from the development team. If you want >> >> something included, you should file a feature request on >> >> redmine.gromacs.org - it's the only official way we keep track of >> fixes >> >> and features. If it's not there, it likely won't get addressed until >> one >> >> of the developers has a compelling need to work on it. >> >> >> >> -Justin >> >> >> >> >> >> On May 1, 2013, at 2:34 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >>> >> >>> >> >>>> >> >>>> On 4/30/13 8:01 PM, Sikandar Mashayak wrote: >> >>>> >> >>>>> Hi >> >>>>> >> >>>>> I found the branch of gromacs code called localpressure-4.0 at >> >>>>> http://redmine.gromacs.org/**projects/gromacs/repository/** >> >>>>> show?rev=localpressure-4-0< >> http://redmine.gromacs.org/projects/gromacs/repository/show?rev=localpressure-4-0 >> > >> >>>>> . >> >>>>> I am wondering whether this code can compute the spatial variation >> of >> >>>>> pressure in given system. And if it does, how stable is this >> branch? Are >> >>>>> there any known issues with it? And any particular reason this is >> not >> >>>>> included in main gromacs releases? >> >>>>> >> >>>>> >> >>>> Lack of documentation has made it very difficult to use, it is >> extremely >> >>>> slow, and no one ever asks about it except once every few years. >> All of >> >>>> those factors make it unlikely to ever incorporate into an actual >> release. >> >>>> Given that the development process has gone on for years in the >> absence of >> >>>> any real interest in the localpressure branch, it's probably more >> trouble >> >>>> than it's worth to get it up and running effectively. >> >>>> >> >>>> -Justin >> >>>> >> >>>> -- >> >>>> ==============================**========== >> >>>> >> >>>> Justin A. Lemkul, Ph.D. >> >>>> Research Scientist >> >>>> Department of Biochemistry >> >>>> Virginia Tech >> >>>> Blacksburg, VA >> >>>> jalemkul[at]vt.edu | (540) 231-9080 >> >>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >>>> >> >>>> ==============================**========== >> >>>> -- >> >>>> gmx-users mailing list gmx-users@gromacs.org >> >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< >> http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >>>> * Please search the archive at http://www.gromacs.org/** >> >>>> Support/Mailing_Lists/Search< >> 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< >> http://www.gromacs.org/Support/Mailing_Lists> >> >>>> >> >>> >> >>> >> >> -- >> >> ==============================**========== >> >> >> >> Justin A. Lemkul, Ph.D. >> >> Research Scientist >> >> Department of Biochemistry >> >> Virginia Tech >> >> Blacksburg, VA >> >> jalemkul[at]vt.edu | (540) 231-9080 >> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> >> >> ==============================**========== >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users< >> http://lists.gromacs.org/mailman/listinfo/gmx-users> >> >> * Please search the archive at http://www.gromacs.org/** >> >> Support/Mailing_Lists/Search< >> 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< >> http://www.gromacs.org/Support/Mailing_Lists> >> >> >> > -- >> > 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 >> >> -- >> 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? 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