Hi gmx-users,<br><br>I tried installing the tool, g_residence.c<br><br>I am using gromacs-4.0.7<br>I copied it to the src/tools. There, I executed make command<br><br># make g_residence<br> <br>cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -I/opt/fftw-3.2.2/include -L/opt/fftw-3.2.2/lib    g_residence.c   -o g_residence<br>

g_residence.c:42:22: fatal error: sysstuff.h: No such file or directory<br>compilation terminated.<br>make: *** [g_residence] Error 1<br><br>How do the tool can be installed?<br><br>Chandan<br clear="all"><br>--<br>Chandan kumar Choudhury<br>

NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Wed, Jul 13, 2011 at 8:24 PM, XAvier Periole <span dir="ltr">&lt;<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">

<div style="word-wrap:break-word"><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><div></div><div class="h5"><div>On Jul 13, 2011, at 2:28 AM, Mark Abraham wrote:</div><br></div></div><blockquote type="cite"><div><div></div><div class="h5"> <div text="#000000" bgcolor="#ffffff">

    On 13/07/2011 5:52 PM, Carla Jamous wrote:    <blockquote type="cite">Dear Xavier,<br>      <br>      my problem is the following:<br>      <br>      I&#39;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 type="cite">As you said, if I google residence time, here&#39;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" target="_blank">particle</a>      spends in a particular system.<br>

      <br>      But I don&#39;t find a tool to calculate this residence time in      gromacs, so I&#39;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 href="mailto:x.periole@rug.nl" target="_blank">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&#39;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><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>                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    <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>

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