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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Received on Fri Aug 04 2023 - 14:00:02 PDT
