[gmx-users] selection around circle

[jkrieger at mrc-lmb.cam.ac.uk]

Does it make sense to install gromacs 5.0 beta for analysing a simulation from 4.6.x?

On 18 Dec 2013, at 05:17, Venkat Reddy <venkat4bt at gmail.com> wrote:

> 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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> 
> 
> 
> -- 
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
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