[gmx-users] Regarding use of harmonic wall model

[Shashank Ranjan Srivastava]

Thank you so much Prof. Lemkul for your reply.
As I don't know what and how to use this pull code, if you have any idea
regarding what you have suggested will be of great help to me.
Meanwhile I will read more about it.

Thank You

On Mon, Apr 20, 2020 at 1:14 AM Justin Lemkul <jalemkul at vt.edu> wrote:

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> On 4/18/20 4:43 AM, Shashank Ranjan Srivastava wrote:
> > Hello everyone,
> > I want to create a gap  between the first and last strand of a beta
> barrel
> > so that I can put a new strand in between.
> > So, I have generated an input file using charmm-gui and using its gromacs
> > production file (production.mdp) to run the simulation. I want to use a
> > harmonic wall model to disrupt the bonding between the first and last
> > strand of the beta barrel but not getting how to do it .
> > I have asked it before as well but I did not get any suggestion.
> > Please kindly help me with this query if anybody has any idea regarding
> > this.
>
> I suggest using the pull code. The implementation of walls in GROMACS
> does not do what you're asking.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
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-- 
Shashank Ranjan Srivastava
Molecular Biophysics Laboratory
Department of Biological Sciences,
IISER-Bhopal,
Madhya Pradesh