Re: about GaMD reweighting

From: Radak, Brian K (
Date: Tue Jun 06 2017 - 11:29:09 CDT

I haven't seen a tutorial, but my understanding was that the "old" aMD output retains its meaning with the new code.

The code snippet your provide looks like it computes a linear response-like approximation to the bias free energy:

f_bias ~= < dU > / kT

which is reportedly accurate for GaMD, although a variance term may also be appropriate. I don't know off-hand whether or not a linear response re-weighting procedure is also recommended - maybe this can be linearized too?

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: <> on behalf of Francesco Pietra <>
Sent: Tuesday, June 6, 2017 10:58:40 AM
Subject: namd-l: about GaMD reweighting


 Does the following aMD reweighting "grep"

# For NAMD simulation:
# grep "ACCELERATED MD" namd.log | awk 'NR%1==0' | awk '{print $6/(0.001987*300)" " $4 " " $6 " "$8}' > weights.dat

apply to GaMD too? Is any tutorial about?


francesco pietra

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