[gmx-users] problem with making index.ndx

Mark Abraham 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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