Hi,<br><br>I have used the command =<br><br>g_dist -f md.xtc -s md.tpr -n index.ndx <br><br>which gives an output of data=<br><br> 0.0000000 0.6259024 0.3880000 0.3610001 -0.3329997<br> 1.0000000 0.6778775 0.2590003 0.5939999 -0.1989999<br>
2.0000000 0.6759030 0.2529998 0.5939999 -0.2000003<br> 3.0000000 0.6463353 0.1690001 0.5680003 -0.2579999<br> 4.0000000 0.6808891 0.2639999 0.6050000 -0.1669998<br> 5.0000000 0.6883561 0.3090000 0.5920000 -0.1670003<br>
6.0000000 0.6201660 0.2769997 0.5139999 -0.2090001<br> 7.0000000 0.6832005 0.2910001 0.5809999 -0.2110000<br> 8.0000000 0.6472999 0.2960002 0.5339999 -0.2150002<br> 9.0000000 0.6542692 0.1880000 0.5400000 -0.3180003<br>
10.0000000 0.6725602 0.3230002 0.5780001 -0.1180000<br> 11.0000000 0.6138712 0.3470001 0.4769998 -0.1700001<br> 12.0000000 0.6999645 0.2860000 0.6150002 -0.1729999<br> 13.0000000 0.6504593 0.1200001 0.6160002 -0.1710000<br>
14.0000000 0.6447160 0.2110000 0.5869999 -0.1629996<br> 15.0000000 0.6645610 0.2040000 0.5710001 -0.2720003<br> 16.0000000 0.6481276 0.2330003 0.5560002 -0.2379999<br> 17.0000000 0.6511113 0.2240002 0.5609999 -0.2430000<br>
18.0000000 0.7119258 0.2650001 0.6220002 -0.2230000<br> 19.0000000 0.6653563 0.0929999 0.6170001 -0.2309999<br> 20.0000000 0.6881638 0.2520001 0.6070004 -0.2040000<br> 21.0000000 0.7161944 0.2090001 0.6220002 -0.2870002<br>
22.0000000 0.6587778 0.1400001 0.6020002 -0.2279997<br> 23.0000000 0.5798631 0.0170002 0.5160003 -0.2639999<br> 24.0000000 0.5862564 0.0390000 0.5239997 -0.2599998<br> 25.0000000 0.6923014 -0.1240001 0.5520000 -0.3990002<br>
26.0000000 0.5787479 -0.0899997 0.5050001 -0.2680001<br> 27.0000000 0.5776323 -0.2589998 0.4730000 -0.2070003<br> 28.0000000 0.5910018 -0.1630001 0.5250001 -0.2170000<br> 29.0000000 0.4448786 -0.1570001 0.4020000 -0.1079998<br>
30.0000000 0.4806164 -0.2160001 0.4000001 -0.1560001<br> 31.0000000 0.5405830 -0.1700001 0.4730000 -0.1989999<br> 32.0000000 0.5614526 -0.1080003 0.4930000 -0.2459998<br> 33.0000000 0.4994450 -0.0730000 0.4500003 -0.2040000<br>
34.0000000 0.5323368 -0.1420002 0.4830003 -0.1730003<br><br><br>From this the first column is the time and the second is the water protein atom distance. so when am using the g_analyze i would use the 1st and 2nd column for the input? More over now this distances are below 0.8 nm . what would i do if my data in between shows distance more than 0.8nm. <br>
<br>Thanks<br><div class="gmail_quote">On Wed, Feb 1, 2012 at 6:48 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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">
<div class="im"><br>
<br>
aiswarya pawar 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 Gromacs Users,<br>
<br>
i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data.<br>
<br>
<br>
</blockquote>
<br></div>
I'm not clear on what you're trying to do. g_analyze performs simple statistical operations (averages, error estimates) on the input data. If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing.<br>
<br>
Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, if necessary.<br>
<br>
-Justin<br>
<br>
--<br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></span></blockquote></div><br><br clear="all"><br>-- <br>Aiswarya B Pawar<br><br><div>Project Assistant,<br>Bioinformatics Dept, <br>Indian Institute of Science<br>Bangalore<br><br></div><br>