[gmx-users] Residence time and trjorder

Baofu Qiao qiaobf at gmail.com
Tue Jul 12 14:32:45 CEST 2011

HI Carla,

I wrote a similar code, see attached. But it is written for my 
condition. You should modify it accordingly.

Baofu Qiao

On 07/12/2011 02:04 PM, Carla Jamous wrote:
> Dear gmx-users,
> I used trjorder in order to study the water molecules that are closer 
> than 5 A from my protein.
> trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb 
> -nshell nshell_.xvg -r 0.5 -b 0 -e 5000
> But now I need to analyse the residence time of a water molecule, I 
> mean the number of times a single water molecule stays in a radius of 
> 5 A of the protein and divide this number by the total number of 
> conformations, in order to have a pourcentage value.
> Please is there any gromacs tool able to do this calculation or else 
> does anyone have an idea of how to do that?
> Thank you
> Carla

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