[gmx-users] Residence time and trjorder

[XAvier Periole]

Mark is right g_dist can help you for this but there is no specific
tool calculating residence time ... I guess everyone dreams of
someone writing it :))

On Jul 13, 2011, at 2:28 AM, Mark Abraham wrote:

> 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 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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