Dear Dr. Cruzeiro
According to your comment, it seems that the setting for how to describe
the transitions between the protonation states in the constant pH MD
calculations can be responsible for the possible failures I have.
I am sorry to say that it is difficult for me to check the setting
because I am new to MD simulations and Amber.
What I did is to just run "make test" for the parallel version of
Amber18/AmberTools19...
Therefore, I will address this problem when I am familiar with MD
simulations and Amber, and the implicit solvent constant pH REMD
calculations are needed for my research.
Thank you for your kind help.
Sincerely,
Kosuke Tachibana
On 2020/03/25 2:13, Cruzeiro, Vinicius wrote:
> Hello Kosuke,
>
> Regarding the issue from February 5, 2020
> (archive.ambermd.org/202002/0055.html), Zoran sent me a direct e-mail
> and I ended up replying to this issue off the list. Here is what I
> wrote to him. I hope this helps.
>
> The failures you are seeing should not be a problem for you. The
> first ones are just one line that is not being printed in the
> mdout file, and the phmd_remd/implicit test that is failing is
> actually coming from a different/separate constant pH
> implementation based on a continuous description of the
> protonation states. I am assuming you are using the CpHMD version
> in the Amber tutorials
> (https://ambermd.org/tutorials/advanced/tutorial18/index.htm),
> which uses a discrete transition between protonation states.
>
>
> Best,
>
> *Vinícius Wilian D. Cruzeiro, PhD*
> Postdoctoral Researcher
> San Diego Supercomputer Center
> Department of Chemistry and Biochemistry
> University of California, San Diego
> Voice: +1(858)246-5584
> ------------------------------------------------------------------------
> *From:* Kosuke Tachibana <tachibana-kosuke.oita-u.ac.jp>
> *Sent:* Tuesday, March 24, 2020 8:57 AM
> *To:* amber.ambermd.org <amber.ambermd.org>
> *Cc:* Cruzeiro, Vinicius <vcruzeiro.UCSD.EDU>
> *Subject:* Re: [AMBER] Installation problem for a parallel version of
> Amber18/AmberTools19
> 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> <mailto:david.case.rutgers.edu>
>> Subject: Re: [AMBER] Installation problem for a parallel version of
>> Amber18/AmberTools19
>> To: AMBER Mailing List<amber.ambermd.org> <mailto:amber.ambermd.org>
>> Cc:vcruzeiro.ucsd.edu <mailto:vcruzeiro.ucsd.edu>
>> Message-ID:
>> <20200323133848.kqc6hwjxnzkjj2xq.vpn-client-172-16-9-226.rutgers.edu> <mailto: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 Wed Mar 25 2020 - 03:00:02 PDT
