[gmx-users] (no subject)
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If you're just starting out, don't use outdated software.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
> 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.
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.
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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