[gmx-users] g_select -select

[Mark Abraham]

On 16/02/2012 6:15 AM, Paymon Pirzadeh wrote:
> Hello,
> I am trying to make an dynamic index file of the hydration shell of my
> protein (hopefully using it with other gromacs tools). I am considering
> up to 10A from protein as the distance needed for my selection.
> I am using g_select with the following format:
>
> g_select -f traj.xtc -s traj.tpr -on hydrationlayer -n -seltype res_com
> -select 'SOL within 10 of protein'
>
> but I get error messages about syntax. How can I select water molecules
> within 10A of my protein then?

Check out "help examples" within g_select, and remember that GROMACS 
doesn't work in Angstroms.

Mark