[gmx-users] fraction of native contacts calculation

[bipin singh]

Thanks for the information.

On Thu, Nov 1, 2012 at 10:56 PM, Justin Lemkul <jalemkul at vt.edu> 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 <erikm at xray.bmc.uu.se>
>> 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<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 6688        fax: +46 18 511 755
>>> erikm at xray.bmc.uu.se
>>> http://www2.icm.uu.se/molbio/**elflab/index.html<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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-- 
-----------------------
*Regards,*
Bipin Singh