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On 2/02/2012 12:28 AM, aiswarya pawar wrote:
<blockquote
cite="mid:CAEa6cRAM_NxVOEx_0GgZSaMPh=ERa3GpcLcywnTjLbyn-egdYQ@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
The above command measures distances between centres of masses of
groups, like g_dist -h says. It doesn't measure "distance between
protein and water atoms within a cut off". You still haven't
described what you're trying to measure, or what your simulation
looks like, so it's impossible to help you.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEa6cRAM_NxVOEx_0GgZSaMPh=ERa3GpcLcywnTjLbyn-egdYQ@mail.gmail.com"
type="cite">
<br>
Thanks<br>
<div class="gmail_quote">On Wed, Feb 1, 2012 at 6:48 PM, Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
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>
========================================<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<span class="HOEnZb"><font
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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>
<br>
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</blockquote>
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