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
estimate persistence length of whole DNA, you have to calculate it for
helical axis of the DNA.

With best regards,
Rajendra

||
|* Rajendra Kumar *|
| PhD Student|
| Max Planck Institute for Biophysical
Chemistryhttp://www.mpibpc.mpg.de/english/start/index.php
 |
| Theoretical and Computational
Biophysicshttp://www.mpibpc.mpg.de/home/grubmueller/index.html,
 |
| Am Fassberg 11, 37077 Goettingen, Germany  |
| Tel.:  +49 551 201 2304|
||


On Sun, Jul 21, 2013 at 11:27 PM, Mohan maruthi sena maruthi.s...@gmail.com
 wrote:

 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 bonds in
 to length(nm)?. Please suggest me a way to solve this.


 Thanks for a reply in advance,


 With 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

-- 
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 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 dna?



Thanks  regards,
Mohan


On Mon, Jul 22, 2013 at 3:35 PM, rajendra kumar rjd...@gmail.com wrote:

 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
 estimate persistence length of whole DNA, you have to calculate it for
 helical axis of the DNA.

 With best regards,
 Rajendra

 ||
 |* Rajendra Kumar *|
 | PhD Student|
 | Max Planck Institute for Biophysical
 Chemistryhttp://www.mpibpc.mpg.de/english/start/index.php
  |
 | Theoretical and Computational
 Biophysicshttp://www.mpibpc.mpg.de/home/grubmueller/index.html,
  |
 | Am Fassberg 11, 37077 Goettingen, Germany  |
 | Tel.:  +49 551 201 2304|
 ||


 On Sun, Jul 21, 2013 at 11:27 PM, Mohan maruthi sena 
 maruthi.s...@gmail.com
  wrote:

  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 bonds
 in
  to length(nm)?. Please suggest me a way to solve this.
 
 
  Thanks for a reply in advance,
 
 
  With 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
 
 --
 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] 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 bonds in
to length(nm)?. Please suggest me a way to solve this.


Thanks for a reply in advance,


With 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