Dear Vinicius,
As I mentioned in my previous email, fixremdcouts.py worked wonderfully for
sorting the cpout files. However, I have an issue when attempting to use
the sorted cpout files for computing protonation state statistics. The
cphstats is unable to process them, presumably because they still contain
the "Time: **********" record.
It seems that I'll need to fix the time records to resolve this problem.
However, I'm a bit confused about the format of the time record. Could you
please explain the significance of the three digits after the decimal point
in the time records in the cpout files? Here's an example of what I'm
referring to:
Time: 578417.*995*
Time: 588400.*195*
Time: 588401.*995*
...
Could you point me to where I can find these three digits after the decimal
point?
Thank you for your help.
Best regards,
Elvira
вт, 8 авг. 2023 г. в 14:45, Elvira Tarasova <elviratarasovachem.gmail.com>:
> Dear Vinicius,
>
> Thank you for your reply. I used fixremdcouts.py as you suggested and it
> worked!
> Thank you very much for your help.
>
> Best regards,
> Elvira
>
> пт, 4 авг. 2023 г. в 17:22, Vinicius Wilian Cruzeiro <vwcruz.stanford.edu
> >:
>
>> Hello Elvira,
>>
>> I am sorry I missed your e-mail before.
>>
>> It is very likely that cphstats is having a problem while trying to parse
>> **** as a float. If you want to use cphstats, you will need to manually
>> correct the time stamps (or write a script to do that).
>>
>> However, you can parse your cpout files using an alternative AmberTool.
>> There is a chance it will not break because of this issue. All you need to
>> run is: fixremdcouts.py --couts *.cpout . To get the full usage details,
>> type: fixremdcouts.py --help
>>
>> I hope this helps. Please let me know if you have any further questions.
>>
>> All the best,
>>
>> *Vinícius Wilian D. Cruzeiro, PhD*
>> Postdoctoral Researcher
>> Department of Chemistry
>> Stanford University
>> Twitter: .vwcruzeiro
>> ------------------------------
>> *From:* Elvira Tarasova via AMBER <amber.ambermd.org>
>> *Sent:* Friday, August 4, 2023 1:50 PM
>> *To:* amber.ambermd.org <amber.ambermd.org>
>> *Subject:* Re: [AMBER] Problem with time records in cpout- files in REMD
>> CpHMD simulation
>>
>> Dear Amber community,
>>
>> I'm reaching out to remind everyone about my previous question, which
>> unfortunately hasn't received any responses yet. I would really appreciate
>> any help or insights you can provide.
>>
>> The question is below:
>>
>>
>>
>>
>> Dear Amber-community,
>>
>> I have a question regarding REMD CpHMD simulation.
>>
>> During my REMD CpHMD simulation (I used Amber 18), which spanned 1500 ns
>> with a pH range from 3.0 to 7.5 and a 0.5 increment, I faced an error
>> related to the cphstats program (cphstats --fix-remd) while preprocessing
>> the cpout-files after the first 1000 ns. The specific error message was as
>> follows:
>>
>>
>> *Did not recognize the format of cpout remd-*_pH3_5_00101.cpout.Error:
>> Cpout file remd-*_pH3_5_00101.cpout is invalid! Skipping.*
>>
>> Upon inspecting the cpout files, I noticed that time records were missing
>> after
>> 1000ns, replaced instead by *"Time: **********"*. The last available time
>> record was "*Time: 999999.990*".
>> I assume that the absence of time records is the root cause of the error.
>> Please, correct me if I am mistaken.
>>
>> Therefore, I would like to ask you if there is a solution to this problem
>> that doesn't involve manually fixing the time records. If there are
>> alternative methods to resolve this issue, I would greatly appreciate your
>> guidance.
>>
>> Furthermore, I would like to understand the significance of the three
>> digits after the decimal point in the time records in cpout-files, as
>> shown
>> in example below:
>> Time: 578417*.995*
>> Time: 588400*.195*
>> Time: 588401*.995*
>> ...
>> And where can I find these three digits after the decimal point in case I
>> need to fix this problem manually?
>>
>> Thank you for your time and support.
>> Best Regards,
>> Elvira
>>
>>
>>
>> ср, 19 июл. 2023 г. в 13:31, Elvira Tarasova <
>> elviratarasovachem.gmail.com>:
>>
>> > Dear Amber-community,
>> >
>> > I have a question regarding REMD CpHMD simulation.
>> >
>> > During my REMD CpHMD simulation (I used Amber 18), which spanned 1500 ns
>> > with a pH range from 3.0 to 7.5 and a 0.5 increment, I faced an error
>> > related to the cphstats program (cphstats --fix-remd) while
>> preprocessing
>> > the cpout-files after the first 1000 ns. The specific error message was
>> as
>> > follows:
>> >
>> >
>> > *Did not recognize the format of cpout remd-*_pH3_5_00101.cpout.Error:
>> > Cpout file remd-*_pH3_5_00101.cpout is invalid! Skipping.*
>> >
>> > Upon inspecting the cpout files, I noticed that time records were
>> missing
>> > after 1000ns, replaced instead by *"Time: **********"*. The last
>> > available time record was "*Time: 999999.990*".
>> > I assume that the absence of time records is the root cause of the
>> error.
>> > Please, correct me if I am mistaken.
>> >
>> > Therefore, I would like to ask you if there is a solution to this
>> problem
>> > that doesn't involve manually fixing the time records. If there are
>> > alternative methods to resolve this issue, I would greatly appreciate
>> your
>> > guidance.
>> >
>> > Furthermore, I would like to understand the significance of the three
>> > digits after the decimal point in the time records in cpout-files, as
>> > shown in example below:
>> > Time: 578417*.995*
>> > Time: 588400*.195*
>> > Time: 588401*.995*
>> > ...
>> > And where can I find these three digits after the decimal point in case
>> I
>> > need to fix this problem manually?
>> >
>> > Thank you for your time and support.
>> > Best Regards,
>> > Elvira
>> >
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Thu Aug 10 2023 - 10:00:02 PDT
