[gmx-users] local pressure

[XAvier Periole]

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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