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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