<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&nbsp;<div>tool calculating residence time ... I guess everyone dreams of&nbsp;</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">&lt;<a moz-do-not-send="true" href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>&gt;</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>            &lt;g_residence.c&gt;--<br>            gmx-users mailing list &nbsp; &nbsp;<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. Use            the<br>            www 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>          <br>          -- <br>          gmx-users mailing list &nbsp; &nbsp;<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. 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 &nbsp;&nbsp;&nbsp;<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>