Hi Dulal,
The name of the .cpin file is specified by -cprestrt in the groupfile. Each replica will generate a unique .cpin, and may use this .cpin file to resume the simulation.
If you’re doing constant pH simulation in explicit solvent, nstlim*numexchg might be an underestimate of total steps because there are solvent relaxation steps after successful changes of a residue’s protonation state.
Hope this helps!
From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Friday, May 10, 2024 at 4:39 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Restarting constant pH replica exchange MD
Dear Experts,
I run constant pH replica exchange molecular dynamics. I have six
replicas. In each replica I set the following parameters.
nstlim=20000, numexchg=20000, (total steps is 20000*20000)
But it takes many days to complete the run. If my run crashes for some
reason, how can I restart the run? Using the "ntwr" option I can generate a
restart file (ncrst) for coordinate (-c option). But how is the "cpin"
restart (-cprestart option) file generated?
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Fri May 10 2024 - 16:30:02 PDT
