[gmx-users] local pressure

[Sikandar Mashayak]

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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