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.
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