[gmx-users] selection around circle

Justin Lemkul jalemkul at vt.edu
Wed Dec 18 01:15:58 CET 2013

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.


>> 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


More information about the gromacs.org_gmx-users mailing list