[gmx-users] Residence time and trjorder

[Carla Jamous]

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.

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> 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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