[gmx-users] g_analyze doubt
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. Thanks -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
Hi, I have used the command = g_dist -f md.xtc -s md.tpr -n index.ndx which gives an output of data= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.0000.67590300.25299980.593 -0.203 3.0000.64633530.16900010.5680003 -0.257 4.0000.68088910.2630.605 -0.1669998 5.0000.68835610.3090.592 -0.1670003 6.0000.62016600.27699970.513 -0.2090001 7.0000.68320050.29100010.580 -0.211 8.0000.64729990.29600020.533 -0.2150002 9.0000.65426920.1880.540 -0.3180003 10.0000.67256020.32300020.5780001 -0.118 11.0000.61387120.34700010.4769998 -0.171 12.0000.69996450.2860.6150002 -0.172 13.0000.65045930.1210.6160002 -0.171 14.0000.64471600.2110.586 -0.1629996 15.0000.66456100.2040.5710001 -0.2720003 16.0000.64812760.23300030.5560002 -0.237 17.0000.6530.22400020.560 -0.243 18.0000.71192580.26500010.6220002 -0.223 19.0000.66535630.0920.6170001 -0.230 20.0000.68816380.25200010.6070004 -0.204 21.0000.71619440.20900010.6220002 -0.2870002 22.0000.65877780.1410.6020002 -0.2279997 23.0000.57986310.01700020.5160003 -0.263 24.0000.58625640.0390.5239997 -0.258 25.0000.6923014 -0.12400010.552 -0.3990002 26.0000.5787479 -0.0870.5050001 -0.2680001 27.0000.5776323 -0.25899980.473 -0.2070003 28.0000.5910018 -0.16300010.5250001 -0.217 29.0000.4448786 -0.15700010.402 -0.1079998 30.0000.4806164 -0.21600010.401 -0.1560001 31.0000.5405830 -0.1710.473 -0.198 32.0000.5614526 -0.10800030.493 -0.2459998 33.0000.4994450 -0.0730.453 -0.204 34.0000.5323368 -0.14200020.4830003 -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 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 | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
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= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.0000.67590300.25299980.593 -0.203 3.0000.64633530.16900010.5680003 -0.257 4.0000.68088910.2630.605 -0.1669998 5.0000.68835610.3090.592 -0.1670003 6.0000.62016600.27699970.513 -0.2090001 7.0000.68320050.29100010.580 -0.211 8.0000.64729990.29600020.533 -0.2150002 9.0000.65426920.1880.540 -0.3180003 10.0000.67256020.32300020.5780001 -0.118 11.0000.61387120.34700010.4769998 -0.171 12.0000.69996450.2860.6150002 -0.172 13.0000.65045930.1210.6160002 -0.171 14.0000.64471600.2110.586 -0.1629996 15.0000.66456100.2040.5710001 -0.2720003 16.0000.64812760.23300030.5560002 -0.237 17.0000.6530.22400020.560 -0.243 18.0000.71192580.26500010.6220002 -0.223 19.0000.66535630.0920.6170001 -0.230 20.0000.68816380.25200010.6070004 -0.204 21.0000.71619440.20900010.6220002 -0.2870002 22.0000.65877780.1410.6020002 -0.2279997 23.0000.57986310.01700020.5160003 -0.263 24.0000.58625640.0390.5239997 -0.258 25.0000.6923014 -0.12400010.552 -0.3990002 26.0000.5787479 -0.0870.5050001 -0.2680001 27.0000.5776323 -0.25899980.473 -0.2070003 28.0000.5910018 -0.16300010.5250001 -0.217 29.0000.4448786 -0.15700010.402 -0.1079998 30.0000.4806164 -0.21600010.401 -0.1560001 31.0000.5405830 -0.1710.473 -0.198 32.0000.5614526 -0.10800030.493 -0.2459998 33.0000.4994450 -0.0730.453 -0.204 34.0000.5323368 -0.14200020.4830003 -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 -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science
Re: [gmx-users] g_analyze doubt
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= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.0000.67590300.25299980.593 -0.203 3.0000.64633530.16900010.5680003 -0.257 4.0000.68088910.2630.605 -0.1669998 5.0000.68835610.3090.592 -0.1670003 6.0000.62016600.27699970.513 -0.2090001 7.0000.68320050.29100010.580 -0.211 8.0000.64729990.29600020.533 -0.2150002 9.0000.65426920.1880.540 -0.3180003 10.0000.67256020.32300020.5780001 -0.118 11.0000.61387120.34700010.4769998 -0.171 12.0000.69996450.2860.6150002 -0.172 13.0000.65045930.1210.6160002 -0.171 14.0000.64471600.2110.586 -0.1629996 15.0000.66456100.2040.5710001 -0.2720003 16.0000.64812760.23300030.5560002 -0.237 17.0000.6530.22400020.560 -0.243 18.0000.71192580.26500010.6220002 -0.223 19.0000.66535630.0920.6170001 -0.230 20.0000.68816380.25200010.6070004 -0.204 21.0000.71619440.20900010.6220002 -0.2870002 22.0000.65877780.1410.6020002 -0.2279997 23.0000.57986310.01700020.5160003 -0.263 24.0000.58625640.0390.5239997 -0.258 25.0000.6923014 -0.12400010.552 -0.3990002 26.0000.5787479 -0.0870.5050001 -0.2680001 27.0000.5776323 -0.25899980.473 -0.2070003 28.0000.5910018 -0.16300010.5250001 -0.217 29.0000.4448786 -0.15700010.402 -0.1079998 30.0000.4806164 -0.21600010.401 -0.1560001 31.0000.5405830 -0.1710.473 -0.198 32.0000.5614526 -0.10800030.493 -0.2459998 33.0000.4994450 -0.0730.453 -0.204 34.0000.5323368 -0.14200020.4830003 -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 Pass this file directly to g_analyze - there's no need for manipulation. You'll get averages of all four distance columns, but of course just take what you need. 0.8 nm . what would i do if my data in between shows distance more than 0.8nm. You said you had g_dist measure distances between protein atoms and the COM of water molecules within 0.8 nm, so I don't see how a distance greater than 0.8 nm is even possible in this case. -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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596 (nm) t: 1469 5369 SOL 20624 OW 0.785377 (nm) t: 1473 5369 SOL 20624 OW 0.763485 (nm) t: 1474 5369 SOL 20624 OW 0.767805 (nm) t: 1475 5369 SOL 20624 OW 0.736003 (nm) t: 1476 5369 SOL 20624 OW 0.707953 (nm) t: 1477 5369 SOL 20624 OW 0.713135 (nm) t: 1478 5369 SOL 20624 OW 0.694042 (nm) t: 1480 5369 SOL 20624 OW 0.733907 (nm) t: 1481 5369 SOL 20624 OW 0.705245 (nm) t: 1482 5369 SOL 20624 OW 0.678473 (nm) t: 1483 5369 SOL 20624 OW 0.6288 (nm) t: 1492 5369 SOL 20624 OW 0.794252 (nm) t: 1496 5369 SOL 20624 OW 0.753049 (nm) t: 1497 5369 SOL 20624 OW 0.782796 (nm) t: 1498 5369 SOL 20624 OW 0.799607 (nm) t: 1499 5369 SOL 20624 OW 0.69987 (nm) t: 1500 5369 SOL 20624 OW 0.763511 (nm) t: 1501 5369 SOL 20624 OW 0.764072 (nm) t: 1502 5369 SOL 20624 OW 0.739181 (nm) t: 1503 5369 SOL 20624 OW 0.70336 (nm) In the above data can be seen that the time frame is not continuos. i.e. only the time at which the protein water distance within 0.8nm are shown. So is it possible to do g_analyze on this? On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
aiswarya pawar wrote: If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596 (nm) t: 1469 5369 SOL 20624 OW 0.785377 (nm) t: 1473 5369 SOL 20624 OW 0.763485 (nm) t: 1474 5369 SOL 20624 OW 0.767805 (nm) t: 1475 5369 SOL 20624 OW 0.736003 (nm) t: 1476 5369 SOL 20624 OW 0.707953 (nm) t: 1477 5369 SOL 20624 OW 0.713135 (nm) t: 1478 5369 SOL 20624 OW 0.694042 (nm) t: 1480 5369 SOL 20624 OW 0.733907 (nm) t: 1481 5369 SOL 20624 OW 0.705245 (nm) t: 1482 5369 SOL 20624 OW 0.678473 (nm) t: 1483 5369 SOL 20624 OW 0.6288 (nm) t: 1492 5369 SOL 20624 OW 0.794252 (nm) t: 1496 5369 SOL 20624 OW 0.753049 (nm) t: 1497 5369 SOL 20624 OW 0.782796 (nm) t: 1498 5369 SOL 20624 OW 0.799607 (nm) t: 1499 5369 SOL 20624 OW 0.69987 (nm) t: 1500 5369 SOL 20624 OW 0.763511 (nm) t: 1501 5369 SOL 20624 OW 0.764072 (nm) t: 1502 5369 SOL 20624 OW 0.739181 (nm) t: 1503 5369 SOL 20624 OW 0.70336 (nm) In the above data can be seen that the time frame is not continuos. i.e. only the time at which the protein water distance within 0.8nm are shown. So is it possible to do g_analyze on this? As I said before, g_analyze can only perform statistical operations on the (numerical) data supplied to it. What you've asked g_dist to do is print a list of any atoms that satisfy the distance criteria. You may get frames where there are none, you may get frames where there are several atoms that work. There's nothing here that g_analyze can do anything with. You can't average apples and oranges and hope to get grapes, though you might go bananas :) Sorry, couldn't resist a bit of fun there... -Justin On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
On 2/02/2012 2:08 AM, aiswarya pawar wrote: If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596 (nm) t: 1469 5369 SOL 20624 OW 0.785377 (nm) t: 1473 5369 SOL 20624 OW 0.763485 (nm) t: 1474 5369 SOL 20624 OW 0.767805 (nm) t: 1475 5369 SOL 20624 OW 0.736003 (nm) t: 1476 5369 SOL 20624 OW 0.707953 (nm) t: 1477 5369 SOL 20624 OW 0.713135 (nm) t: 1478 5369 SOL 20624 OW 0.694042 (nm) t: 1480 5369 SOL 20624 OW 0.733907 (nm) t: 1481 5369 SOL 20624 OW 0.705245 (nm) t: 1482 5369 SOL 20624 OW 0.678473 (nm) t: 1483 5369 SOL 20624 OW 0.6288 (nm) t: 1492 5369 SOL 20624 OW 0.794252 (nm) t: 1496 5369 SOL 20624 OW 0.753049 (nm) t: 1497 5369 SOL 20624 OW 0.782796 (nm) t: 1498 5369 SOL 20624 OW 0.799607 (nm) t: 1499 5369 SOL 20624 OW 0.69987 (nm) t: 1500 5369 SOL 20624 OW 0.763511 (nm) t: 1501 5369 SOL 20624 OW 0.764072 (nm) t: 1502 5369 SOL 20624 OW 0.739181 (nm) t: 1503 5369 SOL 20624 OW 0.70336 (nm) In the above data can be seen that the time frame is not continuos. i.e. only the time at which the protein water distance within 0.8nm are shown. So is it possible to do g_analyze on this? None of the GROMACS tools are a replacement for thinking. What did you want to do with a list of interactions over time that were within 0.8nm? Run g_analyze is not an answer that will help you :) Mark On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze doubt
Hi users, I have data with the time frame and the distances, how will compute the autocorrelation of this. i did g_analyze but still dont understand what should be the y axis data when providing input for g_analyze. please help. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
On 26/09/2011 4:51 PM, aiswarya pawar wrote: Hi users, I have data with the time frame and the distances, how will compute the autocorrelation of this. i did g_analyze but still dont understand what should be the y axis data when providing input for g_analyze. please help. I don't understand your question. Your first sentence implies you know what quantity you want to autocorrelate, and the second implies you don't. g_analyze needs a time series in an .xvg file of some data to compute an autocorrelation. Usually, an .xvg file written by a GROMACS tool is already prepared for such further analysis. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Thanks, On Mon, Sep 26, 2011 at 12:38 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/09/2011 4:51 PM, aiswarya pawar wrote: Hi users, I have data with the time frame and the distances, how will compute the autocorrelation of this. i did g_analyze but still dont understand what should be the y axis data when providing input for g_analyze. please help. I don't understand your question. Your first sentence implies you know what quantity you want to autocorrelate, and the second implies you don't. g_analyze needs a time series in an .xvg file of some data to compute an autocorrelation. Usually, an .xvg file written by a GROMACS tool is already prepared for such further analysis. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
On 26/09/2011 5:10 PM, aiswarya pawar wrote: HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Have you read g_analyze -h and tried it out? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze doubt
Mark, i read the help but i still didnt understand how do i compute the time series for this data, should i use this data as such for the input? Thanks, On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/09/2011 5:10 PM, aiswarya pawar wrote: HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Have you read g_analyze -h and tried it out? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_analyze doubt
What have you tried with g_analyze so far? What was your result? Is it what you expect? If not, why isn't it what you expect? Trying something out is far faster and you learn more than waiting for a response from others that don't know exactly what you are doing. At a first look, the command you want to run is g_analyze -f data.xvg -ac autocorr.xvg as you have a data file with time (x) and variable (y) data and you want the autocorrelation function of the variable data. Have you tried that command? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of aiswarya pawar Sent: Tuesday, 27 September 2011 3:11 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_analyze doubt Mark, i read the help but i still didnt understand how do i compute the time series for this data, should i use this data as such for the input? Thanks, On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.aumailto:mark.abra...@anu.edu.au wrote: On 26/09/2011 5:10 PM, aiswarya pawar wrote: HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Have you read g_analyze -h and tried it out? Mark -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
