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

I suggest using the pull code. The implementation of walls in GROMACS does not do what you're asking.



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

jalem...@vt.edu | (540) 231-3129


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