Re: [AMBER] Constant pH remd

From: He, Amy via AMBER <amber.ambermd.org>
Date: Wed, 21 Feb 2024 20:42:54 +0000

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.*
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Received on Wed Feb 21 2024 - 13:00:02 PST