[gmx-users] selection around circle

[Venkat Reddy]

Hi,
I have had used 5.0 beta version and as far as I know, "gmx gangle"
supports the output from g_select.


On Wed, Dec 18, 2013 at 6:39 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/17/13 7:43 PM, jkrieger at mrc-lmb.cam.ac.uk wrote:
>
>> Thanks Justin,
>>
>> I have tried this and I can a new index file that has an item for each
>> frame with atoms that match the selection. How do I create a single index
>> item and combine it into the main index file for use with other tools such
>> as g_hbond?
>>
>>
> The output of g_select is not fully compatible with any Gromacs tool, at
> least in any pre-5.0 version.  Given that I have had not had time yet to
> fully investigate the current beta, hopefully someone else can say whether
> or not the g_select output is now fully supported by other tools.
>
> -Justin
>
>
>  Best wishes
>> James
>>
>> On 18 Dec 2013, at 00:14, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 12/17/13 1:55 PM, jkrieger at mrc-lmb.cam.ac.uk wrote:
>>>
>>>> I think g_select does something like this. I am trying to do something
>>>> similar: make a selection of water within 5A or so of a residue in my
>>>> protein. Also need help please.
>>>>
>>>
>>> The examples at the end of g_select -select 'help all' pretty well cover
>>> most of these situations.  What have you tried?  What has it given you?
>>>  Something like:
>>>
>>> same residue as resname SOL and within 0.5 of residue X
>>>
>>> provided that residue X is defined within an .ndx file provided on the
>>> command, line should work.  Disclaimer: this is just off the cuff, but
>>> probably pretty close.
>>>
>>> -Justin
>>>
>>>  Dear Gmx Users,
>>>>>
>>>>> I have my carbon nanotube (lenght z axis) with proteins attached to
>>>>> it. I
>>>>> wish to collect RDF of given type of amino acids away from the surface
>>>>> in
>>>>> two dimensions (xy). Z axis does not interest me. That would make a
>>>>> circle
>>>>> then. My question: how to make a specific index group of this circle?
>>>>> Any
>>>>> ideas appreciated.
>>>>>
>>>>> Steven
>>>>> --
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>>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>
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>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
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> Gromacs Users mailing list
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036