[gmx-users] local pressure

[Sikandar Mashayak]

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 <symashayak at gmail.com>wrote:

> Thanks Xavier,
>
> I will give it a try.
>
>
> On Wed, May 1, 2013 at 10:56 AM, XAvier Periole <x.periole at 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 <symashayak at 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 <jalemkul at 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 <jalemkul at 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 at 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-request at 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 at 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-request at 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 at 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-request at gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> --
>> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>