[gmx-users] Residence time and trjorder

XAvier Periole x.periole at rug.nl
Tue Jul 12 17:51:09 CEST 2011

Dear Boafu,

This sounds like a great tool!

Carla, note that once you've ordered the water molecules you loose
the continuity of their trajectories ... that is because you order  
them in
function of their distance to the protein.

I am not sure the definition you give will give you the answer to the
residence time. you can google residence time and proteins and see
what come out :))


On Jul 12, 2011, at 6:32 AM, Baofu Qiao wrote:

> HI Carla,
> I wrote a similar code, see attached. But it is written for my  
> condition. You should modify it accordingly.
> regards,
> 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
> <g_residence.c>--
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