Dear Professor Case,
cc. Dr. Cruzeiro
Thank you for replying to my questions.
> Have you applied all updates? Run "$AMBERHOME/update_amber --help" and
> follow the instructions.
Yes. I confirmed that all the updates have been applied to both Amber18
and AmberTools19.
> The parallel tests were designed to PASS for 2 and 4 MPI threads, so
> you might try that.
I also did the parallel tests for 2 and 4 MPI threads.
I found no possible failures or errors in the tests for 2 MPI threads,
which would be because the tests for the implicit solvent constant pH
REMD were not carried out in the case of 2 MPI threads.
On the other hand, in the tests for 4 MPI threads, the same possible
failures about the implicit solvent constant pH REMD were still found
though the other possible failures disappeared.
> And, if you are not planning to run implicit solvent constant pH REMD
> calculations, you can ignore the problem.
Because I am new to molecular dynamics simulation, I am not sure whether
the implicit solvent constant pH REMD calculations will be used.
Therefore, I will start to use and learn Amber for now. This problem
will be addressed when I need the calculations for my research.
I am sorry that I forgot to send another possible problem about
AmberTools19.
Please kindly find the attached file, which is a part of a log file for
the parallel tests using 4 MPI threads.
Though this problem did not appear as error in the final result, the
messages in the attached file seem to show that there are some problems
with bond information.
This possible problem was also found in the tests using 2 or 8 MPI threads.
If this problem should be addressed, I would be happy if you could let
me know what to do.
Sincerely,
Kosuke Tachibana
> Message: 5
> Date: Mon, 23 Mar 2020 09:38:48 -0400
> From: David A Case<david.case.rutgers.edu>
> Subject: Re: [AMBER] Installation problem for a parallel version of
> Amber18/AmberTools19
> To: AMBER Mailing List<amber.ambermd.org>
> Cc:vcruzeiro.ucsd.edu
> Message-ID:
> <20200323133848.kqc6hwjxnzkjj2xq.vpn-client-172-16-9-226.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Mon, Mar 23, 2020, Kosuke Tachibana wrote:
>> I have some possible failures and errors when I did "make test" for a
>> parallel (MPI) version of Amber18/AmberTools19.
> Have you applied all updates? Run "$AMBERHOME/update_amber --help" and
> follow the instructions.
>
> The parallel tests were designed to PASS for 2 and 4 MPI threads, so you
> might try that. But some of your diffs look like changes in output
> formatting, which led me to ask about updates. Others may have better
> answers here.
>
> And, if you are not planning to run implicit solvent constant pH REMD
> calculations, you can ignore the problem.
>
>> The similar problem was reported by Zoran, which were posted to the
>> Amber Mailing List on February 5 2020.
>> (archive.ambermd.org/202002/0055.html)
>> However, I could not find any answers for the problem in this post.
>>
> Sorry that the older post didn't get resolved. cc-ing to Vinicius in
> case he has ideas here.
>
> ....dac
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Received on Tue Mar 24 2020 - 09:00:02 PDT
