[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Tue Jan 2 13:07:21 CET 2018

On 1/2/18 6:26 AM, Rakesh Mishra wrote:
> Dear all
> I am just a beginner in gromacs. I have installed gromacs 5.1 version.  I

If you're just starting out, don't use outdated software. Use the latest 
official version (2016.4) and be ready for a brand new 2018 release 
sometime soon.

> 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.

There is nothing wrong with this. For every action, there is an equal 
but opposite reaction, after all.

> 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.

If you want an immobile reference for whatever reason, apply position 
restraints to residue 44. You'll need to create a custom restraint file 
with genrestr and a suitable index group, or by hand.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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