[gmx-users] (no subject)

Rakesh Mishra rockinbhu at gmail.com
Tue Jan 2 12:26:17 CET 2018

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
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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