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
>>> AMBER.ambermd.org
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Received on Sat May 11 2024 - 02:00:03 PDT
