[gmx-users] (no subject)

[Rakesh Mishra]

Thanks Justin

I followed your suggestion. now I am able to restrain (immobile) any
molecule during pulling.

thanks for your help.

On Tue, Jan 2, 2018 at 4:56 PM, Rakesh Mishra <rockinbhu at gmail.com> wrote:

> Dear all
>
> I am just a beginner in gromacs. I have installed gromacs 5.1 version.  I
> am doing  pulling for si-rna  (double stranded, 22 nucleotides each ). I
> am applying
> pulling code of  umbrella sampling. Using that, we have chosen 22nd number
> residue of chain A is under pulling with constant velocity rate in +ve x
> direction.  and residue 44 of  apposite chain B at the apposite end is
> taking as reference . Now I am thinking to make the reference residue 44 as
> immobile. But when
> after simulation I am trying to see the trajectory . Then I Am finding that
> the residue n 44 (reference residue of pulling) is also moving and which is
> in apposite direction.
> even it is showing that reference residue 44 is crossing the box wall in
> -ve x direction.
>
> My aim is to pull residue n 22 of chain-A of si-rna by making reference
> residue n 44 of chain-B of si-rnA as a immobile, i mean no need for big
> motion in apposite direction.
>
> --
> * 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 <094736%2062491>, +91877749632*
>



-- 
* 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, +91877749632*