[AMBER] Regarding restarting of Gaussian Accelerated MD.

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Tue, 23 Feb 2021 10:09:04 +0530

Dear all,

I am doing Gaussian Accelerated MD using GPU accelerated version of AMBER18
on a system with 2,00,000 atoms. So the estimated time for completion of
the simulation is around 290hrs for a run of 500ns. We have a wall time
limit of 120 hours and so I want to do the 500ns simulation in smaller
parts. But in doing so I am confused regarding altering the parameters. For
example, ntcmd = 1000000 for our whole run of 500ns. In case I am doing
this as 100ns for 5 runs, how should I alter the parameters like ntcmd and
nteb which are fixed values for the 500ns run. If I use the same script by
just altering the nstlim line, everytime the run might have these many
conventional MD steps, which we do not want. Kindly give any suggestion on

Sruthi Sudhakar

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Received on Mon Feb 22 2021 - 21:00:02 PST
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