From: Alexander Adams (xadams_at_umich.edu)
Date: Fri Apr 06 2018 - 14:08:43 CDT
I am performing a simulation of the transport protein XylE in membrane with
the sugar xylose bound in the central pocket. I am using accelerated MD in
order to access a conformation change on the nanosecond timescale.
Unfortunately, the total potential boost results in the sugar unbinding
from the central pocket central pocket and diffusing away from the protein.
I know there is a form of aMD in Amber that allows for selective
acceleration of just an enzyme, substrate, etc., and was wondering if an
equivalent exists in NAMD.
Thanks in advance!
This archive was generated by hypermail 2.1.6 : Thu Dec 12 2019 - 23:19:42 CST