Hi everyone,<br><br>when am doing this g_dist between the protein and water am getting the distance between water-water. why it is so?? and is there a way i can find distance in each time frame.<br><br>Thanks<br><br><div class="gmail_quote">
On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar <span dir="ltr"><<a href="mailto:aiswarya.pawar@gmail.com">aiswarya.pawar@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 users,<br><br>To get the distance between water and protein i did -<br><br> g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11<br><br>from this i should obtain an output file as distance.xvg which i dont get.<br>
<br>and my output is printed on the terminal as- <br><br>t: 1 136 SOL 2336 OW 0.772373 (nm) <br>t: 1 136 SOL 2337 HW1 0.706358 (nm)<br>t: 1 136 SOL 2338 HW2 0.807787 (nm)<br>t: 1 139 SOL 2345 OW 0.821094 (nm)<br>
t: 1 139 SOL 2346 HW1 0.810919 (nm)<br>t: 1 139 SOL 2347 HW2 0.771526 (nm)<br>t: 1 7237 SOL 23640 HW1 0.997056 (nm)<br>t: 1 11793 SOL 37307 OW 0.868929 (nm)<br>t: 1 11793 SOL 37308 HW1 0.927205 (nm)<br>t: 1 11793 SOL 37309 HW2 0.776699 (nm)<br>
t: 2 125 SOL 2303 OW 0.940527 (nm) <br><br>In this <br><br>t: 1 136 SOL 2336 OW 0.772373 (nm) <br><br>does the 't' states the time frame, 136 SOL states the SOL molecule number and 2336 OW the residue contact from protein and the 0.772373 nm the distance between them.<br>
<br>Thanks<br><br>
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