Re: Missing cphrst file in incomplete run

From: Acharya, Atanu (
Date: Mon Mar 14 2022 - 13:48:58 CDT

Dear Brian,
     Thank you so much for the detailed explanation. I am using the following settings.
cphRun 1000 10000
cphRestartFreq 1000


cphRun 1000 10000
cphRestartFreq 5000

Neither run wrote the cphrst file.

Thank you,

From: <>
Sent: Saturday, March 12, 2022 2:05 PM
To: <>; Acharya, Atanu <>
Subject: Re: namd-l: Missing cphrst file in incomplete run

Hi Atanu,

This does not sound like intended behavior. Can you say a little bit more about what kind of settings you are using (i.e. the specific number of MD/MC cycles and the value of cphRestartFreq)? One possibility is that the Tcl I/O buffer is not getting flushed even though the file is being closed -- that could behavior could be system dependent.

In general I would highly recommend calibrating your settings so that NAMD completes normally in the allowed walltime. Like most MD codes, this has not been aggressively tested for other scenarios. A good way to get a conservative estimate is to estimate the total wall time from the benchmark ns/day, adding ~30% to the cost for the longest possible switch run at each cycle--_000_BN7PR07MB42448FDA376420E0879A3BDCBA0F9BN7PR07MB4244namp_--

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