Selective accelerated MD in NAMD

From: Alexander Adams (xadams_at_umich.edu)
Date: Fri Apr 06 2018 - 14:08:43 CDT

Hello all,

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!
Alex Adams

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