Yes, I think in theory we could make the .cpin file like how the very first .cpin was made, using cpinutil.py. We just have to define the protonation states we want to continue from (which should be able to find at the end of cpout files!
From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Saturday, May 11, 2024 at 4:36 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Restarting constant pH replica exchange MD
Sorry for the speaking mistake. Is there any way to generate cpin file
after certain steps?
Thanking you in advance
On Sat, 11 May 2024, 2:03 pm Dulal Mondal, <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> 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.*
>>> _______________________________________________
>>> AMBER mailing list
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Received on Sat May 11 2024 - 07:00:02 PDT
