[gmx-users] selection around circle

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

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
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
>>> a mail to gmx-users-request at gromacs.org.
> 
> -- 
> ==================================================
> 
> 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
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.