[gmx-users] (no subject)

Vytautas Rakeviius vytautas1987 at yahoo.com
Tue Jan 2 15:31:43 CET 2018

You should give more details how you try to make residue 44 immobile. Keep in mind that some ways to do that can be "defeated" with strong enough pulling. Most likely you just have to try few times with different pulling and restraining options.

    On Tuesday, January 2, 2018, 12:30:59 PM GMT+2, Rakesh Mishra <rockinbhu at gmail.com> wrote:  
 Dear sir

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, +91877749632*
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