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
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
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
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
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
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
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
**
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
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