[gmx-users] selection around circle

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Wed Dec 18 01:43:25 CET 2013


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?

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
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> 
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