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. Thanks On Wed, Feb 1, 2012 at 6:48 PM, Justin A. Lemkul <[email protected]> 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 | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore
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