[gmx-users] problem with making index.ndx
Mark.Abraham at anu.edu.au
Tue Jan 31 08:33:41 CET 2012
On 31/01/2012 6:26 PM, Anushree Tripathi wrote:
> I am using gromacs 4.5.3 version.When I run the command (i.e.,
> make_ndx -f em.gro -o index.ndx),It is not showing any option for DPPC
> group which I want to include.Please tell me how could I merge or
> create this option for proceeding to the next step of NVT simulation.
You will have to make a custom index group. You won't get it magically
supplied. make_ndx prompts you for how to get its online help. Read that
and decide how best you can teach it about the atoms you want in your
DPPC group, depending what is actually present in your coordinate file.
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