[gmx-users] Persistence length of whole DNA molecule
Hi all, I want to calculate the persistence length of whole DNA molecule. I know that we can calculate it by using option g_polystat -f .trr -p p.xvg , but I am not able to figure out what set of of atoms I have to select while making the index, so that I could get persistence length of whole DNA molecule. I have tried by giving backbone atom index for calculation but not getting the correct values ? Please suggest me what atom index I should select which can include helical axis information while calculating the persistence length. Thanks regards, Mohan -- 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] Persistence length of whole DNA molecule
Hi, I have not used g_polystat, and I cannot say about usage of this tool. I observed that you missed two oxygen atoms (O3' and O5') in the backbone atom index. There are several methods for the calculation of persistence length of a polymer, and you may look into literature for theories. For example, you can also use end-to-end distance distribution or radius of gyrations. But, these methods are based on the assumptions, so one should be careful. When DNA bends, helical axis is expected to bend simultaneously. Therefore, I suggested to use the helical axis in the last mail. You can calculate helical axis of the DNA using external tools such as 3DNA and Curves+ . If you will be able to calculate the length of axis over which correlations in the tangents are lost, that length will be persistence length. The persistence length of the DNA is ~40-50 nm. To calculate persistence length is difficult for very small DNA because bending in small DNA is rare in simulations. You may look into the literature for the methods applicable to sub-persistence length polymer. With best regards, Rajendra -- 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] Persistence length of whole DNA molecule
Thank you sir for a reply , I missed those atoms , I will try to replace it and then do it. The out put file contains not length but bonds, It says average persistence length is 4.3 bonds. I do not know how to calculate helical axis, I will try today using 3DNA and let you know. Thank you very much, Mohan Maruthi On Tue, Jul 23, 2013 at 3:59 PM, rajendra kumar rjd...@gmail.com wrote: Hi, I have not used g_polystat, and I cannot say about usage of this tool. I observed that you missed two oxygen atoms (O3' and O5') in the backbone atom index. There are several methods for the calculation of persistence length of a polymer, and you may look into literature for theories. For example, you can also use end-to-end distance distribution or radius of gyrations. But, these methods are based on the assumptions, so one should be careful. When DNA bends, helical axis is expected to bend simultaneously. Therefore, I suggested to use the helical axis in the last mail. You can calculate helical axis of the DNA using external tools such as 3DNA and Curves+ . If you will be able to calculate the length of axis over which correlations in the tangents are lost, that length will be persistence length. The persistence length of the DNA is ~40-50 nm. To calculate persistence length is difficult for very small DNA because bending in small DNA is rare in simulations. You may look into the literature for the methods applicable to sub-persistence length polymer. With best regards, Rajendra -- 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
