[gmx-users] Regarding use of harmonic wall model

[Justin Lemkul]

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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================