Hi Amy!
Thanks so much for the suggestion. Something went wrong in the writing of the cpout files. Here’s what I found:
I went to grep “Solvent pH” and got:
Binary file 001/phremd_1.cpout matches
This is true for all four replicates for this particular run (indexed with “1”).
But when I open he cpout file with vim, it looks like a normal text file.
My next step was to analyze the pH listed for each residue. To do that, I needed to convert the binary files to text files with:
tr -cd '\11\12\15\40-\176' < phremd_1.cpout > phremd_1_text.cpout
Then I ran:
grep -E "Residue\s+[0-9]+\s+State:\s+[0-9]+\s+pH:\s+[0-9]+\.[0-9]+" yourfile.txt | sort -k6,6n
And I found that some of the lines were wrongly formatted; for example:
Residue 9 State: 0 pH: 15.500Residue 21 State: 1 pH: 14.000
Residue 9 State: 0 pH: 15.500RResidue 10 State: 1 pH: 15.500
RResidue 10 State: 1 pH: 15.500
Residue 10 State: 1 pResidue 16 State: 1 pH: 14.500
Residue 19 State: 0 pHResidue 16 State: 1 pH: 15.000
I find similar irregularities in the original file that grep thinks is in binary:
Residue Residue 40 State: 0 pHResidue 2 State: 1 pH: 15.500
It looks to me like something went wrong with the synchronization where multiple processes were writing simultaneously to the file. What do you think?
What troubles me is: Why? I’ve ran dozens of pH-REMD simulations on the same computer and this is the only instance of this problem.
I think I’m going to re-run this simulation. But if there is someway I can know how to prevent whatever happened, that would be great because the simulation takes about a day.
Best,
Matthew
On Aug 18, 2024, at 11:28 PM, He, Amy <he.1768.buckeyemail.osu.edu> wrote:
Hi Matthew! I might be wrong, but I think this warning message often appears when there’s a problem with the first line in the cpout files, “Solvent pH”, which is, when the data in your cpout files contain a pH that’s not reported in the first line of any of the provided cpout files. If you’re very sure that the data in your cpout files are correct, you can re-distribute the data by your own codes without looking at Solvent pH at the beginning.
Best regards,
--
Amy He
Forli Lab . TSRI
yihe.scripps.edu
From: Guberman-Pfeffer, Matthew via AMBER <amber.ambermd.org>
Date: Sunday, August 18, 2024 at 12:02 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Unclear cphstats warning
Dear AMBER community,
I ran a 4-way pH-REMD in two chunks (indexed as 0 and 1). When processing the output form the second of these chunks with the following command:
cphstats --fix-remd reordered_1 001/phremd_1.cpout 002/phremd_1.cpout 003/phremd_1.cpout 004/phremd_1.cpout
I get:
WARNING: not all data records were assigned to a specific cpout file
this can happen, for instance, if you did *not* provide all
of the replica cpout files to cphstats to process. Check
your results carefully!
But I did provide the cpout file for each of the four replicas. Something else is presumably wrong. How can I figure out what is causing the warning? I’ve run the same command in other directories for differ 4-way replicas and many more chunks and get no warning. Something seems to have happened in this particular case.
Best,
Matthew
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Received on Sun Aug 18 2024 - 21:30:01 PDT
