Re: [gmx-users] local pressure

[XAvier Periole]

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  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 
> wrote:
> 
>> Thanks Xavier,
>> 
>> I will give it a try.
>> 
>> 
>> On Wed, May 1, 2013 at 10:56 AM, XAvier Periole  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 
>>> 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  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  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 listgmx-users@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-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>>> http://www.gromacs.org/Support/Mailing_Lists>
>>> 
>> 
>> 
> --
> ==**==
> 
> Justin A. Le

Re: [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 wrote:

> Thanks Xavier,
>
> I will give it a try.
>
>
> On Wed, May 1, 2013 at 10:56 AM, XAvier Periole  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 
>> 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  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  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 listgmx-users@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-requ...@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.bevanla

Re: [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  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 
> 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  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  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 listgmx-users@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-requ...@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 listgmx-users@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.or

Re: [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  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  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  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
> .
> 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
 
 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-users
 * Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Searchbefore
  posting!
 * Please don't post (un)subscribe requests to the list. Use the www
 interface or send it to gmx-users-requ...@gromacs.org.
 * Can't post? Read 
 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
>> 
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>> 
> -- 
> gmx-users mailing listgmx

Re: [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  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  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
 .
 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
>>>
>>> ==**==
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Searchbefore
>>>  posting!
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read 
>>> 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
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] local pressure

[Justin Lemkul]

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  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.
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


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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


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Re: [gmx-users] local pressure

[XAvier Periole]

The use of the original code is quite straightforward, the post processing is a 
bit more confusing but quite accessible. 

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.

On May 1, 2013, at 2:34 AM, Justin Lemkul  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.
>> 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
> 
> 
> -- 
> gmx-users mailing listgmx-users@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-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] local pressure

[Justin Lemkul]

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.
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


--
gmx-users mailing listgmx-users@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 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

[Justin A. Lemkul]

Amit Choubey wrote:

Dear all,

Could anyone direct me to the manual for local pressure calculation or a 
place where everything is mentioned about it ? I have been only able to 
collect bits and pieces from the mailing lists.




That's probably all there is to be found.  There's no manual linked from the git 
web interface or the ftp site.


-Justin


Thank you
Amit

On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote:


On 15/06/2011 9:09 PM, Jianguo Li wrote:

Dear all,

I have made a test calculation of local pressure using version 4.5
for my membrane simulation using CHARMM FF. When rerun the
simulation, mdrun gives the localpressure data. Howeve, instead of
giving an anveraged data of the local pressure, mdrun gives a
separate file for each frame, so I got many files:
localpressure.dat0, localpressure.dat1, localpressure.dat2,
localpressure.dat3 ..
Then I need to calculate the pressure tensor for each frame and
make average. but these localpressure.dat files are very big (each
file is about 30 Mb), occupying large space of the hard disk. Can
anyone give some suggestions on how to fix this? Thank you very much!


I would expect that the output frequency is configurable, but can
only suggest you consult what documentation exists for this version.
Your main alternatives are

* to compress the files with (say) bzip2 or (less effective) gzip
and construct a script to uncompress them singly and analyse them
"on the fly" (AMBER users do a bit of this kind of thing, Google around)
* to discard ones that are too frequent. However, judging from the
numbers below, every 100ps is probably OK.

Mark



The command is:
mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o
box_md5_rerun.trr  -g md5_rerun.log -localpgrid 0.1
And the output message is:

Dumping local pressure based on 1 frames to localpressure.dat0...
Reading frame   2 time 119400.000  


Dumping local pressure based on 1 frames to localpressure.dat1...
Reading frame   3 time 119500.000  


Dumping local pressure based on 1 frames to localpressure.dat2...
Reading frame   4 time 119600.000  


Dumping local pressure based on 1 frames to localpressure.dat3...
Reading frame   5 time 119700.000  


Dumping local pressure based on 1 frames to localpressure.dat4...
Reading frame   6 time 119800.000  
...


Cheers,
Jianguo




*From:* Justin A. Lemkul  <mailto:jalem...@vt.edu>
*To:* Discussion list for GROMACS users 
<mailto:gmx-users@gromacs.org>
*Sent:* Friday, 10 June 2011 07:10:35
*Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5



Amit Choubey wrote:
> Thanks Justin, I tried to install the recent git version but the
configure file is missing. How should I install this version ?
>

Run the bootstrap script.  It generates the configure script.

-Justin

>
> On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul
mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>> wrote:
>
>
>
>Amit Choubey wrote:
>
>Dear all,
>
>I saw an unanswered post at
>   
http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html

>
>It is about calculating local pressure in v 4.5 when using
>CHARMM FF. Could someone give me some pointers about this?
>
>
>I don't know what the development status of version 4.5 is,
but you
>can access it at:
>
>   
http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

>
>It hasn't been merged with release-4-5-patches in some time,
so many
>resolved bugs won't be fixed.
>
>-Justin
>
>--
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080 
>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>--gmx-users mailing listgmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
><mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
>http://lists.gromacs.org/mailman/listinfo/gmx-users
>Please search the arc

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

[Amit Choubey]

Dear all,

Could anyone direct me to the manual for local pressure calculation or a
place where everything is mentioned about it ? I have been only able to
collect bits and pieces from the mailing lists.

Thank you
Amit

On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham wrote:

>  On 15/06/2011 9:09 PM, Jianguo Li wrote:
>
>  Dear all,
>
> I have made a test calculation of local pressure using version 4.5 for my
> membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives
> the localpressure data. Howeve, instead of giving an anveraged data of the
> local pressure, mdrun gives a separate file for each frame, so I got many
> files: localpressure.dat0, localpressure.dat1, localpressure.dat2,
> localpressure.dat3 ..
> Then I need to calculate the pressure tensor for each frame and make
> average. but these localpressure.dat files are very big (each file is about
> 30 Mb), occupying large space of the hard disk. Can anyone give some
> suggestions on how to fix this? Thank you very much!
>
>
> I would expect that the output frequency is configurable, but can only
> suggest you consult what documentation exists for this version. Your main
> alternatives are
>
> * to compress the files with (say) bzip2 or (less effective) gzip and
> construct a script to uncompress them singly and analyse them "on the fly"
> (AMBER users do a bit of this kind of thing, Google around)
> * to discard ones that are too frequent. However, judging from the numbers
> below, every 100ps is probably OK.
>
> Mark
>
>
>  The command is:
> mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o
> box_md5_rerun.trr  -g md5_rerun.log -localpgrid 0.1
> And the output message is:
> 
> Dumping local pressure based on 1 frames to localpressure.dat0...
> Reading frame   2 time 119400.000
>
> Dumping local pressure based on 1 frames to localpressure.dat1...
> Reading frame   3 time 119500.000
>
> Dumping local pressure based on 1 frames to localpressure.dat2...
> Reading frame   4 time 119600.000
>
> Dumping local pressure based on 1 frames to localpressure.dat3...
> Reading frame   5 time 119700.000
>
> Dumping local pressure based on 1 frames to localpressure.dat4...
> Reading frame   6 time 119800.000
> ...
>
> Cheers,
> Jianguo
>
>
>
>  ------
> *From:* Justin A. Lemkul  
> *To:* Discussion list for GROMACS users 
> 
> *Sent:* Friday, 10 June 2011 07:10:35
> *Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5
>
>
>
> Amit Choubey wrote:
> > Thanks Justin, I tried to install the recent git version but the
> configure file is missing. How should I install this version ?
> >
>
> Run the bootstrap script.  It generates the configure script.
>
> -Justin
>
> >
> > On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul  jalem...@vt.edu>> wrote:
> >
> >
> >
> >Amit Choubey wrote:
> >
> >Dear all,
> >
> >I saw an unanswered post at
> >
> http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
> >
> >It is about calculating local pressure in v 4.5 when using
> >CHARMM FF. Could someone give me some pointers about this?
> >
> >
> >I don't know what the development status of version 4.5 is, but you
> >can access it at:
> >
> >
> http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
> >
> >It hasn't been merged with release-4-5-patches in some time, so many
> >resolved bugs won't be fixed.
> >
> >-Justin
> >
> >--
> >
> >Justin A. Lemkul
> >Ph.D. Candidate
> >ICTAS Doctoral Scholar
> >MILES-IGERT Trainee
> >Department of Biochemistry
> >Virginia Tech
> >Blacksburg, VA
> >jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> >
> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> >
> >--gmx-users mailing listgmx-users@gromacs.org
> ><mailto:gmx-users@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-requ...@gromacs.org
> ><mailto:gmx-users-requ...@gromacs.org>.
> >Can't post? Read http://www.gr

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

[Mark Abraham]

On 15/06/2011 9:09 PM, Jianguo Li wrote:

Dear all,

I have made a test calculation of local pressure using version 4.5 for 
my membrane simulation using CHARMM FF. When rerun the simulation, 
mdrun gives the localpressure data. Howeve, instead of giving an 
anveraged data of the local pressure, mdrun gives a separate file for 
each frame, so I got many files: localpressure.dat0, 
localpressure.dat1, localpressure.dat2, localpressure.dat3 ..
Then I need to calculate the pressure tensor for each frame and make 
average. but these localpressure.dat files are very big (each file is 
about 30 Mb), occupying large space of the hard disk. Can anyone give 
some suggestions on how to fix this? Thank you very much!


I would expect that the output frequency is configurable, but can only 
suggest you consult what documentation exists for this version. Your 
main alternatives are


* to compress the files with (say) bzip2 or (less effective) gzip and 
construct a script to uncompress them singly and analyse them "on the 
fly" (AMBER users do a bit of this kind of thing, Google around)
* to discard ones that are too frequent. However, judging from the 
numbers below, every 100ps is probably OK.


Mark


The command is:
mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o 
box_md5_rerun.trr  -g md5_rerun.log -localpgrid 0.1

And the output message is:

Dumping local pressure based on 1 frames to localpressure.dat0...
Reading frame   2 time 119400.000

Dumping local pressure based on 1 frames to localpressure.dat1...
Reading frame   3 time 119500.000

Dumping local pressure based on 1 frames to localpressure.dat2...
Reading frame   4 time 119600.000

Dumping local pressure based on 1 frames to localpressure.dat3...
Reading frame   5 time 119700.000

Dumping local pressure based on 1 frames to localpressure.dat4...
Reading frame   6 time 119800.000
...

Cheers,
Jianguo




*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Friday, 10 June 2011 07:10:35
*Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5



Amit Choubey wrote:
> Thanks Justin, I tried to install the recent git version but the 
configure file is missing. How should I install this version ?

>

Run the bootstrap script.  It generates the configure script.

-Justin

>
> On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu 
<mailto:jalem...@vt.edu>>> wrote:

>
>
>
>Amit Choubey wrote:
>
>Dear all,
>
>I saw an unanswered post at
> http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
>
>It is about calculating local pressure in v 4.5 when using
>CHARMM FF. Could someone give me some pointers about this?
>
>
>I don't know what the development status of version 4.5 is, but you
>can access it at:
>
> 
http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

>
>It hasn't been merged with release-4-5-patches in some time, so many
>resolved bugs won't be fixed.
>
>-Justin
>
>--
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>--gmx-users mailing list gmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org>

> <mailto:gmx-users@gromacs.org <mailto:gmx-users@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-requ...@gromacs.org 
<mailto:gmx-users-requ...@gromacs.org>
> <mailto:gmx-users-requ...@gromacs.org 
<mailto:gmx-users-requ...@gromacs.org>>.

>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- gmx-users mailing list gmx-users@gromacs.org 
<mailto:gmx-users@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!
Ple

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

[Jianguo Li]

Dear all,

I have made a test calculation of local pressure using version 4.5 for my 
membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the 
localpressure data. Howeve, instead of giving an anveraged data of the local 
pressure, mdrun gives a separate file for each frame, so I got many files: 
localpressure.dat0, localpressure.dat1, localpressure.dat2, localpressure.dat3 
..
Then I need to calculate the pressure tensor for each frame and make average. 
but  these localpressure.dat files are very big (each file is about 30 Mb), 
occupying large space of the hard disk. Can anyone give some suggestions on how 
to fix this? Thank you very much!

The command is: 
mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o box_md5_rerun.trr  
-g md5_rerun.log -localpgrid 0.1
And the output message is:

Dumping local pressure based on 1 frames to localpressure.dat0...
Reading frame   2 time 119400.000   

Dumping local pressure based on 1 frames to localpressure.dat1...
Reading frame   3 time 119500.000   

Dumping local pressure based on 1 frames to localpressure.dat2...
Reading frame   4 time 119600.000   

Dumping local pressure based on 1 frames to localpressure.dat3...
Reading frame   5 time 119700.000   

Dumping local pressure based on 1 frames to localpressure.dat4...
Reading frame   6 time 119800.000   
...

Cheers,
Jianguo







From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Friday, 10 June 2011 07:10:35
Subject: Re: [gmx-users] local pressure calcuation for Gromacs-4.5



Amit Choubey wrote:
> Thanks Justin, I tried to install the recent git version but the configure 
> file 
>is missing. How should I install this version ?
> 

Run the bootstrap script.  It generates the configure script.

-Justin

> 
> On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote:
> 
> 
> 
> Amit Choubey wrote:
> 
> Dear all,
> 
> I saw an unanswered post at
>http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
> 
> It is about calculating local pressure in v 4.5 when using
> CHARMM FF. Could someone give me some pointers about this?
> 
> 
> I don't know what the development status of version 4.5 is, but you
> can access it at:
> 
>
>http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
> 
> It hasn't been merged with release-4-5-patches in some time, so many
> resolved bugs won't be fixed.
> 
> -Justin
> 
> -- 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> 
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- gmx-users mailing listgmx-users@gromacs.org
> <mailto:gmx-users@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-requ...@gromacs.org
> <mailto:gmx-users-requ...@gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- gmx-users mailing listgmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing listgmx-users@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 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

[Justin A. Lemkul]

Amit Choubey wrote:
Thanks Justin, I tried to install the recent git version but the 
configure file is missing. How should I install this version ?




Run the bootstrap script.  It generates the configure script.

-Justin



On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul > wrote:




Amit Choubey wrote:

Dear all,

I saw an unanswered post at
http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html

It is about calculating local pressure in v 4.5 when using
CHARMM FF. Could someone give me some pointers about this?


I don't know what the development status of version 4.5 is, but you
can access it at:


http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

It hasn't been merged with release-4-5-patches in some time, so many
resolved bugs won't be fixed.

-Justin

-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] local pressure calcuation for Gromacs-4.5

[Amit Choubey]

Thanks Justin, I tried to install the recent git version but the configure
file is missing. How should I install this version ?


On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Dear all,
>>
>> I saw an unanswered post at
>> http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
>>
>> It is about calculating local pressure in v 4.5 when using CHARMM FF.
>> Could someone give me some pointers about this?
>>
>>
> I don't know what the development status of version 4.5 is, but you can
> access it at:
>
>
> http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
>
> It hasn't been merged with release-4-5-patches in some time, so many
> resolved bugs won't be fixed.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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Re: [gmx-users] local pressure calcuation for Gromacs-4.5

[Justin A. Lemkul]

Amit Choubey wrote:

Dear all,

I saw an unanswered post at 


http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html

It is about calculating local pressure in v 4.5 when using CHARMM FF. 
Could someone give me some pointers about this?




I don't know what the development status of version 4.5 is, but you can access 
it at:


http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

It hasn't been merged with release-4-5-patches in some time, so many resolved 
bugs won't be fixed.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] local pressure calculation

[Mark Abraham]

anirban polley wrote:

Hi,
Is anyone have done local pressure calculation of a membrane by 
standard package gromacs-localp? Could you please show me the the .mdp 
file for it?


I would start by reading its documentation. The GROMACS version on which 
this is based is so old that probably nobody on this list still recalls 
how to use it.


Mark
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RE: [gmx-users] local pressure

[Dallas B. Warren]

I would recommend you have a read through the appendix in the GROMACS
manual titled "Manual Pages".  This has all the scripts provided with
GROMACS and the manual page for them, which describes what each one
does.  Reading through that will go a long way to letting you know what
you can and can't do with the GROMACS scripts.  If can't find it there,
then search at
http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ (which
is where I found the answer to your last question).  Then, if after
that, still can't find out how to do it, fire a question to this
emailing list.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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Re: [gmx-users] Local pressure profiles

[Philip Shushkov]

In fact I tried this first, but the message was quite disappointing:

Fatal error: 3921wat.5ns.oneside.pot.all.trr.trj does not exist.

I could not make the program to read in the file in trr format because it
always required the trj format. I am sorry but I have no experience with the
old versions of GROMACS. May be it is a stupid mistake but I could not
resolve the issue.

Philip



2008/6/5 David van der Spoel <[EMAIL PROTECTED]>:

> Philip Shushkov wrote:
>
>> Dear Prof. van der Spoel,
>>
>> I have made new *.tpb file with the old grompp version after some changes
>> of the simulation parameters such as switching to cut-off electrostatics and
>> replacing lincs with shake, but now I think that I have problem with the
>> trajectory file. I converted the trr file into trj file as is required by
>> the program using the trjconv program. My pbc seem to be normal in the
>> trajectory file because the simulation was carried out in NVT ensemble but
>> when starting the mdrun patched with local pressure code I received the
>> following message:
>>
>> trn version: GMX_trn_file
>> Reading frame   0 time0.000   Warning: Only triclinic boxes with
>> the first vector parallel to the x-axis and the second vector in the
>> xy-plane are supported.
>> Box (3x3):
>>Box[0]={5.3e-315,  0.0e+00, 5.3e-315}
>>Box[1]={ 0.0e+00, 5.43969e-315,  0.0e+00}
>>Box[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
>> Can not fix pbc.
>>
>> And in the log file the pbc that were read from tpb file are:
>>
>> box (3x3):
>>   box[0]={ 4.88021e+00,  0.0e+00,  0.0e+00}
>>   box[1]={ 0.0e+00,  4.88021e+00,  0.0e+00}
>>   box[2]={ 0.0e+00,  0.0e+00,  2.0e+01}
>>
>> I hope that there is a solution of the obstacle again.
>> Thank you very much in advance for your help.
>>
>> Best regards,
>> Philip
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> Have you tried with the trr file? I don't see why it should not work.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>
> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Local pressure profiles

[David van der Spoel]

Philip Shushkov wrote:

Dear Prof. van der Spoel,

I have made new *.tpb file with the old grompp version after some 
changes of the simulation parameters such as switching to cut-off 
electrostatics and replacing lincs with shake, but now I think that I 
have problem with the trajectory file. I converted the trr file into trj 
file as is required by the program using the trjconv program. My pbc 
seem to be normal in the trajectory file because the simulation was 
carried out in NVT ensemble but when starting the mdrun patched with 
local pressure code I received the following message:


trn version: GMX_trn_file
Reading frame   0 time0.000   Warning: Only triclinic boxes with 
the first vector parallel to the x-axis and the second vector in the 
xy-plane are supported.

 Box (3x3):
Box[0]={5.3e-315,  0.0e+00, 5.3e-315}
Box[1]={ 0.0e+00, 5.43969e-315,  0.0e+00}
Box[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
 Can not fix pbc.

And in the log file the pbc that were read from tpb file are:

box (3x3):
   box[0]={ 4.88021e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  4.88021e+00,  0.0e+00}
   box[2]={ 0.0e+00,  0.0e+00,  2.0e+01}

I hope that there is a solution of the obstacle again.
Thank you very much in advance for your help.

Best regards,
Philip
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Have you tried with the trr file? I don't see why it should not work.

--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Local pressure profiles

[Philip Shushkov]

Dear Prof. van der Spoel,

I have made new *.tpb file with the old grompp version after some changes of
the simulation parameters such as switching to cut-off electrostatics and
replacing lincs with shake, but now I think that I have problem with the
trajectory file. I converted the trr file into trj file as is required by
the program using the trjconv program. My pbc seem to be normal in the
trajectory file because the simulation was carried out in NVT ensemble but
when starting the mdrun patched with local pressure code I received the
following message:

trn version: GMX_trn_file
Reading frame   0 time0.000   Warning: Only triclinic boxes with the
first vector parallel to the x-axis and the second vector in the xy-plane
are supported.
 Box (3x3):
Box[0]={5.3e-315,  0.0e+00, 5.3e-315}
Box[1]={ 0.0e+00, 5.43969e-315,  0.0e+00}
Box[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
 Can not fix pbc.

And in the log file the pbc that were read from tpb file are:

box (3x3):
   box[0]={ 4.88021e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  4.88021e+00,  0.0e+00}
   box[2]={ 0.0e+00,  0.0e+00,  2.0e+01}

I hope that there is a solution of the obstacle again.
Thank you very much in advance for your help.

Best regards,
Philip


2008/5/30 David van der Spoel <[EMAIL PROTECTED]>:

> Philip Shushkov wrote:
>
>> Dear gmx-users,
>>
>> I would like to calculate the local pressure profile of lipid bilayer and
>> that's why I downloaded and installed the gromacs-localp package that was
>> contributed to the gromacs software by Lindahl and Edholm. The problem is
>> that I have already generated the trajectory of the bilayer and I would like
>> to rerun the simulation in order to recalculate the pressure profile.
>> However, the package I have downloaded is an old version of the gromacs
>> software and when I tried to read in the Version 3.3.3 tpb generated with
>> tpbconv from the original  *.tpr file I received the following error:
>>
>> Fatal error: reading tpx file (5ns.oneside.pot.restart.tpb) version 40
>> with version 20 program.
>>
>> I would like to ask whether there is a way to get around the problem and
>> has someone else encountered such a problem.
>>
>>  just make a tpr with the old gromacs.
>
>  Best regards,
>> Philip
>>
>>
>> 
>>
>> ___
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>
>
> --
> David.
> 
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone:  46 18 471 4205  fax: 46 18 511 755
> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
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