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
> > >
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> > --
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> > V.T. and Louise Jackson Professor in Chemistry
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--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Wed Feb 21 2024 - 22:00:02 PST
