Re: [gmx-users] Persistence length of whole DNA molecule

2013-07-23 Thread mohan maruthi
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

Re: [gmx-users] Persistence length of whole DNA molecule

2013-07-23 Thread rajendra kumar
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 exa

[gmx-users] Persistence length of whole DNA molecule

2013-07-23 Thread Mohan maruthi sena
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 o

Re: [gmx-users] Persistence length calculation using g_polystat

2013-07-22 Thread Mohan maruthi sena
Hello Sir, Thank you very much for a reply. I have selected following atoms P, C5',C4',C3' atoms to estimate persistence length. I want to find persistence length of whole dna, can you please elaborate on , how to calculate persistence length of whole dna using helical axis of the

Re: [gmx-users] Persistence length calculation using g_polystat

2013-07-22 Thread rajendra kumar
Which group of atoms you have taken for the persistence length? g_polystat requires a group of atoms which are consecutively bonded in polymer main-chain. You should take only backbone atoms of one strand of the DNA. But, it does not give the persistence length for the whole DNA. I guess, to estima

[gmx-users] Persistence length calculation using g_polystat

2013-07-21 Thread Mohan maruthi sena
Dear gmx users, I would like to calculate persistence length of DNA using gromacs command g_polystat . The out put file of persists.xvg contains persistence length in number of bonds and it shows that the average persistence length = 4.3 bonds. How can we convert no of b

Re: [gmx-users] persistence length

2006-06-07 Thread David van der Spoel
syma wrote: Hi, I was just wondering if it is possible to calculate the persistence length of a long chain-like molecule with one of the gromacs analysis programs or if anyone has anything else that will do this? Plz give a definition (equation) Thanks in advance, -Syma **

[gmx-users] persistence length

2006-06-07 Thread syma
Hi, I was just wondering if it is possible to calculate the persistence length of a long chain-like molecule with one of the gromacs analysis programs or if anyone has anything else that will do this? Thanks in advance, -Syma *** Dr Syma Khalid