[gmx-users] g_analyze doubt
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Feb 1 14:34:12 CET 2012
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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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