<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Mark is right g_dist can help you for this but there is no specific <div>tool calculating residence time ... I guess everyone dreams of </div><div>someone writing it :))<br><div><div><br><div><div>On Jul 13, 2011, at 2:28 AM, Mark Abraham wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div text="#000000" bgcolor="#ffffff"> On 13/07/2011 5:52 PM, Carla Jamous wrote: <blockquote cite="mid:CADWXoG=SwXRhzEDUWmne++mkb1vWFp23ZLjooswyjs-OuQ-gUw@mail.gmail.com" type="cite">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> </blockquote> <br> 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.<br> <br> Mark<br> <br> <blockquote cite="mid:CADWXoG=SwXRhzEDUWmne++mkb1vWFp23ZLjooswyjs-OuQ-gUw@mail.gmail.com" type="cite">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 moz-do-not-send="true" 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 moz-do-not-send="true" 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 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 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> <g_residence.c>--<br> gmx-users mailing list <a moz-do-not-send="true" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a moz-do-not-send="true" href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a moz-do-not-send="true" href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br> Please don't post (un)subscribe requests to the list. 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Use thewww interface or send it to <a moz-do-not-send="true" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a moz-do-not-send="true" href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br> </blockquote> </div> <br> </blockquote> <br> </div> -- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br></div></div></div></body></html>