[gmx-users] (no subject)
rockinbhu at gmail.com
Fri Jan 5 06:55:31 CET 2018
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*
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