Hi Nitin,
It sounds like the results in the cpout files (before concatenation and any other manipulation) do agree with the outcomes of cphstats. Therefore, this might not be a processing problem. Have you considered visualizing some snapshots (or maybe the endpoint structures) of the subsequent chunks? Do they look substantially different from the first segment of your simulation? Sometimes the preferred protonation state changes because of some conformational change (formation of a salt bridge for example). I feel that some visualization might be helpful for determining the cause of the issue.
Best regards,
Amy
From: Nitin Kulhar <bo18resch11002.iith.ac.in>
Date: Sunday, August 11, 2024 at 10:41 PM
To: He, Amy <he.1768.buckeyemail.osu.edu>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cphstats processing of pH-REMD 'chunks'
Hi Dr Amy Sorry for the late response. I can see it in the cpout files (of all the replicas in the first chunk of MD) that the protonation is toggling amongst all the possible states in accord with the pH value. However, this is not so for the
Hi Dr Amy
Sorry for the late response.
I can see it in the cpout files (of all the replicas
in the first chunk of MD) that the protonation
is toggling amongst all the possible states in
accord with the pH value.
However, this is not so for the subsequent
chunks of MD, wherein the deprotonated state
has become seemingly 'fixed' regardless of
the pH value, which is changing with the
replica-exchange attempts (the successful ones).
Therefore, I would deeply appreciate any help
in pointing out the source of error. Please let
me know if I need to share more information.
Thanks and regards
Nitin Kulhar
On Wed, Aug 7, 2024 at 1:24 AM He, Amy <he.1768.buckeyemail.osu.edu<mailto:he.1768.buckeyemail.osu.edu>> wrote:
Hi Nitin,
It seems like the fraction of protonation from the concatenated files is very low. To confirm if there’s a trend of decreased protonation:
For the individual chunks of simulations, you can run cphstats for the original cpout files. If you know the length of each chunk, the total fraction of protonation can be calculated as a weighted average. No concatenation needed.
If it doesn’t look like an expected trend, maybe it’s due to the concatenation. You can compared with the weighted average and see if you’re concatenating in the way you actually want.
From: Nitin Kulhar <bo18resch11002.iith.ac.in<mailto:bo18resch11002.iith.ac.in>>
Date: Tuesday, August 6, 2024 at 9:37 AM
To: He, Amy <he.1768.buckeyemail.osu.edu<mailto:he.1768.buckeyemail.osu.edu>>, AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] cphstats processing of pH-REMD 'chunks'
Hi Amy Thanks for the email. I apologise for any confusion caused by the term 'chunks'. To clarify, I was NOT referring to the various interval-based averages namely, cumulative, running, and chunk, that can be obtained from cphstats.
Hi Amy
Thanks for the email.
I apologise for any confusion
caused by the term 'chunks'.
To clarify, I was NOT referring to
the various interval-based
averages namely, cumulative,
running, and chunk, that can be
obtained from cphstats.
I meant 'chunk' in the context of
Jason Swail's tutorial on pH-REMD:
http://jswails.wikidot.com/ph-remd#toc10<
https://urldefense.com/v3/__http:/jswails.wikidot.com/ph-remd*toc10__;Iw!!KGKeukY!0QPqWCdXnVdLe8rKHuhDQJUoHGhMynPyu-b40QIv63g2Os1e-DpK5_jKEPGP4bL9_uzoA0pBmpXdBHrl_s3gAVsi_QK48jQAXHEKQHKF$>
To quote from the tutorial:
If you have run 10 ns of simulation
in 1 ns chunks, you will need to
run this program 10 times!
PFA two titration curves: one obtained from
by processing just the first segment, the other
obtained by processing concatenated cpouts
from all segments.
Thanks and regards
Nitin Kulhar
On Mon, Aug 5, 2024 at 4:35 AM He, Amy <he.1768.buckeyemail.osu.edu<mailto:he.1768.buckeyemail.osu.edu>> wrote:
Hi Nitin,
Why do you think the results are wrong? Did it cumulate, or not cumulate, or not space in the way you want?
The manual will give you a detailed difference with examples for the Cumulative, running, and “chunk” options of cphstats.
From: Nitin Kulhar via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
Date: Friday, August 2, 2024 at 9:38 PM
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: [AMBER] cphstats processing of pH-REMD 'chunks'
Dear all
I performed pH-REMD of 8
REPLICAS. 25 ns of REMD
were run in 1 ns SEGMENTS
(or chunks) as delineated in
the tutorial by Jason Swails
available at link <
https://urldefense.com/v3/__http://jswails.wikidot.com/ph-remd__;!!KGKeukY!yNeLxboggV6vrz65BXBmJdJtWYdmVZcrdIOV1wBGc78GZvpfjF_-WCNsdRPGRjBJUhH7F7YBvR3VSKHDhd3UMV574E0$<
https://urldefense.com/v3/__http:/jswails.wikidot.com/ph-remd__;!!KGKeukY!yNeLxboggV6vrz65BXBmJdJtWYdmVZcrdIOV1wBGc78GZvpfjF_-WCNsdRPGRjBJUhH7F7YBvR3VSKHDhd3UMV574E0$> >.
*The problem:*
The pKa values obtained by
processing the cpout files from
all SEGMENTS (or chunks)
were questionable, nay, wrong.
However, the pKa values obtained
by processing the cpout file from
the first SEGMENT alone were
correct.
*Salient details of the REMD:*
The inputs for each SEGMENT
were generated by the
genremdinputs.py script.
The cpin and starting coordinates
for REPLICA 'i' of SEGMENT 'j'
were respectively the cprestart
and restart files generated by
REPLICA 'i' during SEGMENT 'j-1'.
While the seed (ig) value
differed among REPLICAS
of the same SEGMENT, it
was the same for a given
REPLICA in all SEGMENTS.
(Is that genremdinputs.py's doing?)
*Salient details of processing cpouts:*
The cpout files from consecutive
SEGMENTS were concatenated
with the cat command. This was
done for each REPLICA separately.
The concatenated cpout files of ALL
REPLICAS were sorted according to
pH values by using cphstats program
with the --fix-remd option.
The pH-sorted cpout files from above
were processed with cphstats to obtain
pKa values and population data.
Please help me spot the mistake
in my logic or execution of the steps.
Thanks and regards
Nitin Kulhar
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Received on Mon Aug 12 2024 - 21:00:02 PDT
