[gmx-users] (no subject)

[Rakesh Mishra]

Dear Justin its your  conversation  regarding pulling of dsDNA.
Because gromacs is replying as there message is too big so cant be send
and due to that I can not replied in orginal conversation.
But I want to start from the last conversation.

from your side

"It seems to me you have two steps to perform:

1. Extend the duplex to a "ladder-like" conformation
2. Slide one strand past the other

In step 1, I would set the reaction coordinate to be the vector connecting
the terminal *base pairs* (not just one base in one DNA chain) and pull
along that vector in all dimensions. The force will primarily act in one
Cartesian dimension, but by doing it this way, you never have to assume (or
hope) that your system stays nicely aligned along one axis. The pulling
will take some time, and rotation to some extent is inevitable.

In step 2, once the duplex is fully extended, you should be able to do what
you were proposing before, using the terminal single base of each DNA
strand. Again, I still think it's problematic to assume a biasing force in
only one dimension, but that's for you to test.

I'm sorry that I don't have time to look at all the files you sent off-list
or read all the papers you linked. But this is what I can offer as a
suggestion. It's a very difficult system to deal with.

-Justin "


Now my query .

Thanks  for  your lot discussion and advise. So can you tell me please, for
Step First
{In step 1, I would set the reaction coordinate to be the vector connecting
the terminal *base pairs* (not just one base in one DNA chain) and pull
along that vector in all dimensions. The force will primarily act in one
Cartesian dimension, but by doing it this way, you never have to assume (or
hope) that your system stays nicely aligned along one axis. The pulling
will take some time, and rotation to some extent is inevitable.}


(just suggested above) for stretching helical into stretched form of dsDNA
, how this protocol can be modified.


pull_ngroups               = 2
pull_ncoords               = 1
pull_group1_name        = r_24         ; 3' of  chain B of dsDNA as a
reference gorup (not  fixed)
pull_group2_name        = r_12          ;  3' of  chain A of dsDNA as a
pulling gorup
pull_coord1_type          = umbrella      ; harmonic biasing force
pull_coord1_geometry   = distance      ; simple distance increase
pull_coord1_groups       = 1  2
pull_coord1_dim           = Y  N  N
pull_coord1_rate          = 0.005          ; 0.005 nm per ps = 5nm per 1 ns
pull_coord1_k              = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start         = yes           ; define initial COM distance > 0


And other question for which I really bother is that how it is possible to
apply this pull protocol of gromacs
in order to pull two gorups in apposite direction along the pulling
direction. Hoping for response

-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *

*Phone n. +91 9473662491, +918777496532*