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
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