[gmx-users] Re: make_ndx

T.A.Wassenaar T.A.Wassenaar at rug.nl
Fri Jul 1 21:29:10 CEST 2005

Hi Sri,

It is not possible to do this in gromacs. Pymol can make 
such selections, but then you need a script to write an 
index file from a Pymol selection. If you know a bit of 
python that shouldn't be too hard.

Hope it helps,


On Fri, 1 Jul 2005 09:33:36 -0400
  VISWANADHA SRIDHARA <vsrid001 at odu.edu> wrote:
> Hi GMX users,
> I was wondering whether there is any option in make_ndx 
>to get the index of
> the atoms(or molecules) as a function of the box 
> In other words, can I get the index of the molecules 
>separately which are
> 1nm spherical radius in a 3nm cube as an example.(say 
>cube's center is the
> sphere's center too).
> Thanks in advance,
> Sri
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. 
>Use the 
> www interface or send it to 
>gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list