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"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></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'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'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'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" target="_blank">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><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> <g_residence.c>--<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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