[gmx-users] local pressure

[Sikandar Mashayak]

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>
> >>>>
> >>>> ==============================**==========
> >>>> --
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> >>>
> >>>
> >> --
> >> ==============================**==========
> >>
> >> 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>
> >>
> >> ==============================**==========
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