[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 <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
>>>
>>> ========================================
>>> --
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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
>>
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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

========================================