[gmx-users] g_select problem

[Albert]

On 09/28/2013 09:42 AM, rajat desikan wrote:
> Hi,
> I am not sure, but try resname SOL or something similar. Also, your first
> line has waterO and second line has water0.

Hi Rajat:

thanks a lot for such kind and helpful comments. It works now. I run it 
by command:

  g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf 
select.dat -os size.xvg -oc cfrac.xvg -oi index.dat

I am trying to make density of the water molecules inside my protein by 
g_density:

g_density_mpi -f ../md_pbc_center.xtc -s ../md.tpr -ei density.ndx -o 
density.xvg -n density.ndx

but it asked me which water molecules I would like to make..... Do you 
have any idea how to do this correctly?

thank you very much.

best
Albert