[gmx-users] Residence time and trjorder

[Mark Abraham]

On 13/07/2011 5:52 PM, Carla Jamous wrote:
> Dear Xavier,
>
> my problem is the following:
>
> I'm trying to figure out if a water molecule is present in a specific 
> area around my protein and if so, which water molecule is that and how 
> long does it stay in that place.

I think g_dist does this for a group containing a single water molecule. 
All you need to do write a script to iterate over each molecule, and 
then collate the statistics.

Mark

> As you said, if I google residence time, here's the definition: 
> *Residence time* (also known as *removal time*) is the average amount 
> of time that a particle <http://en.wikipedia.org/wiki/Particle> spends 
> in a particular system.
>
> But I don't find a tool to calculate this residence time in gromacs, 
> so I'm trying to find a trick that can give me a pourcentage of the 
> time of my simulation where a certain water molecule stays in the 
> specific area of my protein.
>
> Regards,
> Carla
>
> On Tue, Jul 12, 2011 at 5:51 PM, XAvier Periole <x.periole at rug.nl 
> <mailto:x.periole at rug.nl>> wrote:
>
>
>     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 :))
>
>     XAvier.
>
>
>     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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