<br>Hi Baofu,<br><br>Please can you tell me how to install g_residence.c in gromacs?<br><br>If I understood well, the line command is the following:<br><br>g_residence -s toplogy.tpr -f trajectory.xtc -o output<br><br>What is the format of the output?<br>
<br>Thank you,<br>Carla<br><br><div class="gmail_quote">On Tue, Jul 12, 2011 at 2:32 PM, Baofu Qiao <span dir="ltr"><<a href="mailto:qiaobf@gmail.com">qiaobf@gmail.com</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;">
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><font color="#888888">
Baofu Qiao</font><div><div></div><div class="h5"><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></blockquote></div><br>