Re: [gmx-users] fraction of native contacts calculation

[bipin singh]

Thanks a lot Sanku for your help.

On Thu, Nov 1, 2012 at 11:38 PM, Sanku M  wrote:

> Bipin,
>   There might be a workaround. You might want to check out Plumed plugin
> in latest versions of VMD for calculating fractions of native contact. You
> can load the gromacs trajectory along with the native .gro file in VMD and
> use Plumed plugin inbuilt in VMD . You need to install plumed most probably
> early.
>
>
>
> 
>  From: bipin singh 
> To: Discussion list for GROMACS users 
> Sent: Thursday, November 1, 2012 1:23 PM
> Subject: Re: [gmx-users] fraction of native contacts calculation
>
> Thanks for your response. Hope to see this feature in upcoming GROMACS
> release. Before that, could it be possible to get the modified code in the
> user contribution section, it may be useful for many GROMACS users.
>
>
> On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund 
> wrote:
>
> >
> > 31 okt 2012 kl. 13.43 skrev Justin Lemkul:
> >
> > >
> > >
> > > On 10/31/12 6:02 AM, bipin singh wrote:
> > >> Hello all,
> > >>
> > >> Is there any way to calculate fraction of native contacts during the
> > >> simulation in gromacs. I searched the archives but didn't found any
> > >> significant clue.
> > >
> > > At present, there is no way to do this.  Likely one could modify the
> > g_mindist code to do this - it would be a very nice feature.
> > >
> >
> > If one could get the -sel option of g_hbond to work again then you would
> > get such information with -contact.
> >
> > Erik
> >
> >
> > > -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
> >
> > ---
> > Erik Marklund, PhD
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,75124 Uppsala, Sweden
> > phone:+46 18 471 6688fax: +46 18 511 755
> > er...@xray.bmc.uu.se
> > http://www2.icm.uu.se/molbio/elflab/index.html
> >
> > --
> > 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!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> ---
> *Regards,*
> Bipin Singh
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] fraction of native contacts calculation

[bipin singh]

Thanks a lot Oliver for the useful information.

On Fri, Nov 2, 2012 at 12:26 AM, Oliver Beckstein  wrote:

> >>> Is there any way to calculate fraction of native contacts during the
> >>> simulation in gromacs. I searched the archives but didn't found any
> >>> significant clue.
> >>
> >> At present, there is no way to do this.  Likely one could modify the
> g_mindist code to do this - it would be a very nice feature.
> >>
> >
> > If one could get the -sel option of g_hbond to work again then you would
> get such information with -contact.
> >
>
> In the meantime you might be able to use MDAnalysis
> http://mdanalysis.googlecode.com/ and the native contact analysis in
> MDAnalysis.analysis.contacts, see
> http://packages.python.org/MDAnalysis/documentation_pages/analysis/contacts.html
>
> (If you have questions about MDAnalysis then please ask them on that
> project's discussion group
> http://groups.google.com/group/mdnalysis-discussion — people there are
> more than happy to help.)
>
> Best wishes,
> Oliver
>
> --
> Oliver Beckstein * oliver.beckst...@asu.edu
> http://becksteinlab.physics.asu.edu/
>
> Arizona State University
> Department of Physics
> Tempe, AZ 85287-1504
> USA
>
> Office: PSF 348
> Phone: +1 (480) 727-9765
> FAX: +1 (480) 965-4669
>
> Department of Physics:
> http://physics.asu.edu/home/people/faculty/oliver-beckstein
> Center for Biological Physics:
> http://biophysics.asu.edu/CBP/person.php?ID=343
>
>
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



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*Regards,*
Bipin Singh
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Re: [gmx-users] fraction of native contacts calculation

[Oliver Beckstein]

>>> Is there any way to calculate fraction of native contacts during the
>>> simulation in gromacs. I searched the archives but didn't found any
>>> significant clue.
>> 
>> At present, there is no way to do this.  Likely one could modify the 
>> g_mindist code to do this - it would be a very nice feature.
>> 
> 
> If one could get the -sel option of g_hbond to work again then you would get 
> such information with -contact.
> 

In the meantime you might be able to use MDAnalysis 
http://mdanalysis.googlecode.com/ and the native contact analysis in 
MDAnalysis.analysis.contacts, see 
http://packages.python.org/MDAnalysis/documentation_pages/analysis/contacts.html

(If you have questions about MDAnalysis then please ask them on that project's 
discussion group http://groups.google.com/group/mdnalysis-discussion — people 
there are more than happy to help.)

Best wishes,
Oliver

--
Oliver Beckstein * oliver.beckst...@asu.edu
http://becksteinlab.physics.asu.edu/

Arizona State University
Department of Physics
Tempe, AZ 85287-1504
USA

Office: PSF 348
Phone: +1 (480) 727-9765
FAX: +1 (480) 965-4669

Department of Physics: 
http://physics.asu.edu/home/people/faculty/oliver-beckstein
Center for Biological Physics: http://biophysics.asu.edu/CBP/person.php?ID=343






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Re: [gmx-users] fraction of native contacts calculation

[Sanku M]

Bipin,
  There might be a workaround. You might want to check out Plumed plugin in 
latest versions of VMD for calculating fractions of native contact. You can 
load the gromacs trajectory along with the native .gro file in VMD and use 
Plumed plugin inbuilt in VMD . You need to install plumed most probably early.




 From: bipin singh 
To: Discussion list for GROMACS users  
Sent: Thursday, November 1, 2012 1:23 PM
Subject: Re: [gmx-users] fraction of native contacts calculation
 
Thanks for your response. Hope to see this feature in upcoming GROMACS
release. Before that, could it be possible to get the modified code in the
user contribution section, it may be useful for many GROMACS users.


On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund  wrote:

>
> 31 okt 2012 kl. 13.43 skrev Justin Lemkul:
>
> >
> >
> > On 10/31/12 6:02 AM, bipin singh wrote:
> >> Hello all,
> >>
> >> Is there any way to calculate fraction of native contacts during the
> >> simulation in gromacs. I searched the archives but didn't found any
> >> significant clue.
> >
> > At present, there is no way to do this.  Likely one could modify the
> g_mindist code to do this - it would be a very nice feature.
> >
>
> If one could get the -sel option of g_hbond to work again then you would
> get such information with -contact.
>
> Erik
>
>
> > -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 list    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.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
> --
> gmx-users mailing list    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!
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> 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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Bipin Singh
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Re: [gmx-users] fraction of native contacts calculation

[bipin singh]

Thanks for the information.

On Thu, Nov 1, 2012 at 10:56 PM, Justin Lemkul  wrote:

>
>
> On 11/1/12 1:23 PM, bipin singh wrote:
>
>> Thanks for your response. Hope to see this feature in upcoming GROMACS
>> release. Before that, could it be possible to get the modified code in the
>> user contribution section, it may be useful for many GROMACS users.
>>
>>
> If someone writes the code, certainly.  Gromacs is a user-driven
> community, after all :)
>
> If there is a feature you want, file a feature request on
> redmine.gromacs.org, otherwise no one is likely to pay much attention to
> it, as other, much larger changes are ongoing.
>
> -Justin
>
>
>
>> On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund 
>> wrote:
>>
>>
>>> 31 okt 2012 kl. 13.43 skrev Justin Lemkul:
>>>
>>>

 On 10/31/12 6:02 AM, bipin singh wrote:

> Hello all,
>
> Is there any way to calculate fraction of native contacts during the
> simulation in gromacs. I searched the archives but didn't found any
> significant clue.
>

 At present, there is no way to do this.  Likely one could modify the

>>> g_mindist code to do this - it would be a very nice feature.
>>>


>>> If one could get the -sel option of g_hbond to work again then you would
>>> get such information with -contact.
>>>
>>> Erik
>>>
>>>
>>>  -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

>>>
>>> --**-
>>> Erik Marklund, PhD
>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>> Husargatan 3, Box 596,75124 Uppsala, Sweden
>>> phone:+46 18 471 6688fax: +46 18 511 755
>>> er...@xray.bmc.uu.se
>>> http://www2.icm.uu.se/molbio/**elflab/index.html
>>>
>>> --
>>> 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
>
> ==**==
> --
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-- 
---
*Regards,*
Bipin Singh
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Re: [gmx-users] fraction of native contacts calculation

[Justin Lemkul]

On 11/1/12 1:23 PM, bipin singh wrote:

Thanks for your response. Hope to see this feature in upcoming GROMACS
release. Before that, could it be possible to get the modified code in the
user contribution section, it may be useful for many GROMACS users.



If someone writes the code, certainly.  Gromacs is a user-driven community, 
after all :)


If there is a feature you want, file a feature request on redmine.gromacs.org, 
otherwise no one is likely to pay much attention to it, as other, much larger 
changes are ongoing.


-Justin



On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund  wrote:



31 okt 2012 kl. 13.43 skrev Justin Lemkul:




On 10/31/12 6:02 AM, bipin singh wrote:

Hello all,

Is there any way to calculate fraction of native contacts during the
simulation in gromacs. I searched the archives but didn't found any
significant clue.


At present, there is no way to do this.  Likely one could modify the

g_mindist code to do this - it would be a very nice feature.




If one could get the -sel option of g_hbond to work again then you would
get such information with -contact.

Erik



-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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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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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] fraction of native contacts calculation

[bipin singh]

Thanks for your response. Hope to see this feature in upcoming GROMACS
release. Before that, could it be possible to get the modified code in the
user contribution section, it may be useful for many GROMACS users.


On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund  wrote:

>
> 31 okt 2012 kl. 13.43 skrev Justin Lemkul:
>
> >
> >
> > On 10/31/12 6:02 AM, bipin singh wrote:
> >> Hello all,
> >>
> >> Is there any way to calculate fraction of native contacts during the
> >> simulation in gromacs. I searched the archives but didn't found any
> >> significant clue.
> >
> > At present, there is no way to do this.  Likely one could modify the
> g_mindist code to do this - it would be a very nice feature.
> >
>
> If one could get the -sel option of g_hbond to work again then you would
> get such information with -contact.
>
> Erik
>
>
> > -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
>
> ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 6688fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
---
*Regards,*
Bipin Singh
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Re: [gmx-users] fraction of native contacts calculation

[Erik Marklund]

31 okt 2012 kl. 13.43 skrev Justin Lemkul:

> 
> 
> On 10/31/12 6:02 AM, bipin singh wrote:
>> Hello all,
>> 
>> Is there any way to calculate fraction of native contacts during the
>> simulation in gromacs. I searched the archives but didn't found any
>> significant clue.
> 
> At present, there is no way to do this.  Likely one could modify the 
> g_mindist code to do this - it would be a very nice feature.
> 

If one could get the -sel option of g_hbond to work again then you would get 
such information with -contact.

Erik


> -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!
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> or send it to gmx-users-requ...@gromacs.org.
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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Re: [gmx-users] fraction of native contacts calculation

[Justin Lemkul]

On 10/31/12 6:02 AM, bipin singh wrote:

Hello all,

Is there any way to calculate fraction of native contacts during the
simulation in gromacs. I searched the archives but didn't found any
significant clue.


At present, there is no way to do this.  Likely one could modify the g_mindist 
code to do this - it would be a very nice feature.


-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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[gmx-users] fraction of native contacts calculation

[bipin singh]

Hello all,

Is there any way to calculate fraction of native contacts during the
simulation in gromacs. I searched the archives but didn't found any
significant clue.
*--
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Thanks and Regards,
Bipin Singh*
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