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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 [email protected] >>>> 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 [email protected]. >>>> * 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 [email protected] >> 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 [email protected]. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
