[gmx-users] local pressure

XAvier Periole x.periole at rug.nl
Thu May 2 08:59:00 CEST 2013 

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 <symashayak at 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 <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>
>>>>>>> 
>>>>>>> ==============================**==========
>>>>>>> --
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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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