[gmx-users] index file

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 30 14:56:10 CEST 2011

Elisabeth wrote:
> Dear gromacs users,
> I am planning to produce C-C rdf for my system and I have difficulty 
> making the index file with a group of all C in the system, [Carbon] . 
> .If there are thousands of atoms in the system do I have to go through 
> the top file and note down C atom numbers and use those numbers to make 
> a group in the index file? What is the easiest way of doing this using 
> make_ndx features..

Using "a C*" at the make_ndx prompt should accomplish what you want.  Type 
"help" at the prompt for more advanced examples.


> Thank you for your hints..


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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