What are you looking for? Have a look at the papers they might be inspiring :))
On May 1, 2013, at 10:33 PM, Sikandar Mashayak <symasha...@gmail.com> wrote: > 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? 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? 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? Read http://www.gromacs.org/Support/Mailing_Lists