On 2/02/2012 12:28 AM, aiswarya pawar wrote:
Hi,
I have used the command =
g_dist -f md.xtc -s md.tpr -n index.ndx
which gives an output of data=
0.0000000 0.6259024 0.3880000 0.3610001 -0.3329997
1.0000000 0.6778775 0.2590003 0.5939999 -0.1989999
2.0000000 0.6759030 0.2529998 0.5939999 -0.2000003
3.0000000 0.6463353 0.1690001 0.5680003 -0.2579999
4.0000000 0.6808891 0.2639999 0.6050000 -0.1669998
5.0000000 0.6883561 0.3090000 0.5920000 -0.1670003
6.0000000 0.6201660 0.2769997 0.5139999 -0.2090001
7.0000000 0.6832005 0.2910001 0.5809999 -0.2110000
8.0000000 0.6472999 0.2960002 0.5339999 -0.2150002
9.0000000 0.6542692 0.1880000 0.5400000 -0.3180003
10.0000000 0.6725602 0.3230002 0.5780001 -0.1180000
11.0000000 0.6138712 0.3470001 0.4769998 -0.1700001
12.0000000 0.6999645 0.2860000 0.6150002 -0.1729999
13.0000000 0.6504593 0.1200001 0.6160002 -0.1710000
14.0000000 0.6447160 0.2110000 0.5869999 -0.1629996
15.0000000 0.6645610 0.2040000 0.5710001 -0.2720003
16.0000000 0.6481276 0.2330003 0.5560002 -0.2379999
17.0000000 0.6511113 0.2240002 0.5609999 -0.2430000
18.0000000 0.7119258 0.2650001 0.6220002 -0.2230000
19.0000000 0.6653563 0.0929999 0.6170001 -0.2309999
20.0000000 0.6881638 0.2520001 0.6070004 -0.2040000
21.0000000 0.7161944 0.2090001 0.6220002 -0.2870002
22.0000000 0.6587778 0.1400001 0.6020002 -0.2279997
23.0000000 0.5798631 0.0170002 0.5160003 -0.2639999
24.0000000 0.5862564 0.0390000 0.5239997 -0.2599998
25.0000000 0.6923014 -0.1240001 0.5520000 -0.3990002
26.0000000 0.5787479 -0.0899997 0.5050001 -0.2680001
27.0000000 0.5776323 -0.2589998 0.4730000 -0.2070003
28.0000000 0.5910018 -0.1630001 0.5250001 -0.2170000
29.0000000 0.4448786 -0.1570001 0.4020000 -0.1079998
30.0000000 0.4806164 -0.2160001 0.4000001 -0.1560001
31.0000000 0.5405830 -0.1700001 0.4730000 -0.1989999
32.0000000 0.5614526 -0.1080003 0.4930000 -0.2459998
33.0000000 0.4994450 -0.0730000 0.4500003 -0.2040000
34.0000000 0.5323368 -0.1420002 0.4830003 -0.1730003
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.
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.
Mark
Thanks
On Wed, Feb 1, 2012 at 6:48 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
aiswarya pawar wrote:
Dear Gromacs Users,
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.
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.
Please provide a more clear description of what you are doing,
including all relevant commands, and examples of the data files,
if necessary.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Aiswarya B Pawar
Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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