Dear Xavier,<br><br>my problem is the following:<br><br>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.<br>
<br>As you said, if I google residence time, here's the definition: <b>Residence time</b> (also known as <b>removal time</b>) is the average amount of time that a <a href="http://en.wikipedia.org/wiki/Particle" title="Particle">particle</a> spends in a particular system.<br>
<br>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.<br>
<br>Regards,<br>Carla<br><br><div class="gmail_quote">On Tue, Jul 12, 2011 at 5:51 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Dear Boafu,<br>
<br>
This sounds like a great tool!<br>
<br>
Carla, note that once you've ordered the water molecules you loose<br>
the continuity of their trajectories ... that is because you order them in<br>
function of their distance to the protein.<br>
<br>
I am not sure the definition you give will give you the answer to the<br>
residence time. you can google residence time and proteins and see<br>
what come out :))<br>
<br>
XAvier.<div><div></div><div class="h5"><br>
<br>
On Jul 12, 2011, at 6:32 AM, Baofu Qiao wrote:<br>
<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
HI Carla,<br>
<br>
I wrote a similar code, see attached. But it is written for my condition. You should modify it accordingly.<br>
<br>
regards,<br>
Baofu Qiao<br>
<br>
On 07/12/2011 02:04 PM, Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear gmx-users,<br>
<br>
I used trjorder in order to study the water molecules that are closer than 5 A from my protein.<br>
<br>
trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb -nshell nshell_.xvg -r 0.5 -b 0 -e 5000<br>
<br>
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.<br>
<br>
Please is there any gromacs tool able to do this calculation or else does anyone have an idea of how to do that?<br>
<br>
Thank you<br>
<br>
Carla<br>
</blockquote>
<br></div></div>
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