Is there any way for generation of coin file after completion certain step?
On Sat, 11 May 2024, 2:00 pm Dulal Mondal, <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> Thank you for your response.
>
> On Sat, 11 May 2024, 4:41 am He, Amy, <he.1768.buckeyemail.osu.edu> wrote:
>
>> 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 Sat May 11 2024 - 02:00:02 PDT
