Thank you. I understood my mistake.
On Thu, Feb 22, 2024 at 11:24 AM Dulal Mondal <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> Thank you for your reply. I tried the grep command on my files and this is
> the output I got:
> "grep -m1 'Solvent pH:' ../001/cpout.rep.001 ../002/cpout.rep.001
> ../003/cpout.rep.001 ../004/cpout.rep.001 ../005/cpout.rep.001
> ../006/cpout.rep.001 ../007/cpout.rep.001 ../008/cpout.rep.001
> ../009/cpout.rep.001 ../010/cpout.rep.001
> ../001/cpout.rep.001:Solvent pH: 6.40000
> ../002/cpout.rep.001:Solvent pH: 5.70000
> ../003/cpout.rep.001:Solvent pH: 5.60000
> ../004/cpout.rep.001:Solvent pH: 5.90000
> ../005/cpout.rep.001:Solvent pH: 5.80000
> ../006/cpout.rep.001:Solvent pH: 6.10000
> ../007/cpout.rep.001:Solvent pH: 6.00000
> ../008/cpout.rep.001:Solvent pH: 6.30000
> ../009/cpout.rep.001:Solvent pH: 6.20000
> ../010/cpout.rep.001:Solvent pH: 5.90000"
>
> I can see two files showing the same pH values of 5.9, although I am
> unable to understand a few things over here. How exactly is the grep
> command allocating a specific pH value to a cpout file?
>
> On Thu, Feb 22, 2024 at 2:12 AM He, Amy <he.1768.buckeyemail.osu.edu>
> wrote:
>
>> Hi Dulal,
>>
>>
>>
>> A quick way to find two replicas with the same pH is to print the initial
>> “Solvent pH” in the individual cpout files, something like this:
>>
>> *grep* *-m1* *'Solvent pH:'* ../001/cpout.rep.001 ../002/cpout.rep.001
>> ../003/cpout.rep.001 ../004/cpout.rep.001 ../005/cpout.rep.001
>> ../006/cpout.rep.001 ../007/cpout.rep.001 ../008/cpout.rep.001
>> ../009/cpout.rep.001 ../010/cpout.rep.001*
>>
>>
>>
>> cphstats can’t handle two replicas with the same pH. With these, the
>> sizes of samples at each pH will become unequal, and that can change the
>> error estimates of the pKa fitting, too.. although in my opinion it’s not
>> wrong to have replicas this close (it’s just like the extreme case of
>> unequally spaced replicas)
>>
>>
>>
>> But if this is not something you planned, make sure to check the inputs
>> and outputs. Do you have multiple files that match ../010/cpout.rep.001*?
>> Also, cphstats tries to make sure each replica has a unique pH, but it
>> can’t tell whether the outputs were from the same replica exchange
>> calculation or not. So we need to make sure these are correct
>>
>>
>>
>> Hope this is mildly helpful!
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>> Amy He
>>
>> Hadad Lab . OSU
>>
>> He.1768.osu.edu
>>
>>
>>
>>
>>
>> *From: *Dulal Mondal via AMBER <amber.ambermd.org>
>> *Date: *Wednesday, February 21, 2024 at 1:46 AM
>> *To: *Adrian Roitberg <roitberg.ufl.edu>, AMBER Mailing List <
>> amber.ambermd.org>
>> *Subject: *Re: [AMBER] Constant pH remd
>>
>>
>>
>> Not clear sir.
>>
>> On Tue, 20 Feb, 2024, 11:38 pm Adrian Roitberg via AMBER, <
>> amber.ambermd.org>
>> wrote:
>>
>> > the error is clear, right ?
>> >
>> >
>> > Error: Same pH (5.9) found twice!
>> >
>> >
>> >
>> >
>> >
>> > On 2/20/24 5:16 AM, Dulal Mondal via AMBER wrote:
>> > > [External Email]
>> > >
>> > > Dear Experts,
>> > > I run the constant pH remd with 10 replicas from pH 5.5 to 6.4 with
>> 0.1
>> > pH
>> > > gap. I type the following command
>> > > *cphstats --fix-remd prod001 ../001/cpout.rep.001 ../002/cpout.rep.001
>> > > ../003/cpout.rep.001 ../004/cpout.rep.001 ../005/cpout.rep.001
>> > > ../006/cpout.rep.001 ../007/cpout.rep.001 ../008/cpout.rep.001
>> > > ../009/cpout.rep.001 ../010/cpout.rep.001*
>> > > But it show the following error message.
>> > > Error: Same pH (5.9) found twice!
>> > > Thanking You
>> > > --
>> > > *With regards,*
>> > > *Dulal Mondal,*
>> > > *Research Scholar,*
>> > > *Department of Chemistry,*
>> > > *IIT Kharagpur, Kharagpur 721302.*
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > >
>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2m0EMW4bCEjJifX24_plQ504saKXGYNH1CQ-BHZDLVfm0VCPE4zxvSu70KoA-Ynr7Rim3tqfdhIabyM_0uXUHltqnoA$
>> <https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2m0EMW4bCEjJifX24_plQ504saKXGYNH1CQ-BHZDLVfm0VCPE4zxvSu70KoA-Ynr7Rim3tqfdhIabyM_0uXUHltqnoA$>
>> >
>> > --
>> > Dr. Adrian E. Roitberg
>> > V.T. and Louise Jackson Professor in Chemistry
>> > Department of Chemistry
>> > University of Florida
>> > roitberg.ufl.edu
>> > 352-392-6972
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> >
>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2m0EMW4bCEjJifX24_plQ504saKXGYNH1CQ-BHZDLVfm0VCPE4zxvSu70KoA-Ynr7Rim3tqfdhIabyM_0uXUHltqnoA$
>> <https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2m0EMW4bCEjJifX24_plQ504saKXGYNH1CQ-BHZDLVfm0VCPE4zxvSu70KoA-Ynr7Rim3tqfdhIabyM_0uXUHltqnoA$>
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>>
>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2m0EMW4bCEjJifX24_plQ504saKXGYNH1CQ-BHZDLVfm0VCPE4zxvSu70KoA-Ynr7Rim3tqfdhIabyM_0uXUHltqnoA$
>> <https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!2m0EMW4bCEjJifX24_plQ504saKXGYNH1CQ-BHZDLVfm0VCPE4zxvSu70KoA-Ynr7Rim3tqfdhIabyM_0uXUHltqnoA$>
>>
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 21 2024 - 23:00:02 PST
