[gmx-users] selection around circle

[Justin Lemkul]

On 12/18/13 3:33 AM, jkrieger at mrc-lmb.cam.ac.uk wrote:
> Does it make sense to install gromacs 5.0 beta for analysing a simulation from 4.6.x?
>

The 4.6.x series can't handle the g_select output (different index groups for 
each frame), so it's not really possible to (easily) make use of it.  One could, 
of course, write a script to dump out every frame separately, run the analysis 
on that frame using the corresponding index group, then assemble the output into 
something useful.  But if 5.0 beta does all of that seamlessly, why wouldn't you 
take advantage of that?

-Justin

> 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
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
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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
>>>
>>> ==================================================
>>> --
>>> 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
>> --
>> Gromacs Users mailing list
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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

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