Re: restarting Gaussian accelerated MD fails

From: Miao, Yinglong (miao_at_ku.edu)
Date: Tue Jan 22 2019 - 14:10:21 CST

On Jan 22, 2019, at 2:56 AM, Vlad Cojocaru <vlad.cojocaru_at_mpi-muenster.mpg.de<mailto:vlad.cojocaru_at_mpi-muenster.mpg.de>> wrote:

I also have a question regarding the k0 values. During the gAMD equilibration, these values are updated at each time step whereas during a production run , k0 is maintained constant throughout the simulation ... That is correct, right ?

Dear Vlad,

Yes, k0 works in the way as you described.

Hope David can help with the simulation restart problem, and Andrew on the step number in the restart file (Should it be the number used to calculate average and standard deviation of the boost potential?)

Best wishes,
Yinglong

Yinglong Miao, Ph.D.
Assistant Professor
Center for Computational Biology and
Department of Molecular Biosciences
University of Kansas
http://miao.compbio.ku.edu

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