Thanks for sharing that link!
I’ll have a look and will get back to you if I have encountered some problems.
Thanks again,
Muhammad
From: Liao <liaojunzhuo.aliyun.com>
Sent: Saturday, 21 December 2019 6:08 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] How to use AMBER on Supercomputer
Are you talking about something like this:
“ #PBS -l walltime=04:00:00
#PBS -l nodes=2:ppn=28
#PBS -j oe
#PBS -q long
set workdir = "~/AMBER_Tutorial/003.SANDER"
cd ${workdir}
“
There are sample scripts that run on a supercomputer on the Rizzo tutorial,
http://ringo.ams.stonybrook.edu/index.php/2019_AMBER_tutorial_with_PDBID_2BXF<
http://ringo.ams.stonybrook.edu/index.php/2019_AMBER_tutorial_with_PDBID_2BXF>
. Thanks.
Also welcoming answers on my GPU suggestions question.
Sent from my iPhone
> On Dec 21, 2019, at 9:51 AM, MUHAMMAD KHATTAB FATHI KHATTAB <100030036.student.swin.edu.au<mailto:100030036.student.swin.edu.au>> wrote:
>
> Dear James,
>
> Thanks for your response!
>
> What I meant is, what files should I use.
> For example, when I was using GAUSSIAN on supercomputer, I had to prepare script file and input file.
> IN the script file I had to specify the walltime, no. of processors,…etc
> In the input file, I have to specify the route section to run certain calculation.
>
> So what is the case with AMBER???????
>
>
> Thanks,
> Muhammad
>
> From: Liao <liaojunzhuo.aliyun.com<mailto:liaojunzhuo.aliyun.com>>
> Sent: Saturday, 21 December 2019 5:28 PM
> To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
> Subject: Re: [AMBER] How to use AMBER on Supercomputer
>
> As far as I know your supercomputer needs to have AMBER installed on it, and then you remote logon to it (usually via ssh).
>
> I also have a different question for fellow users, somehow the mailing list is rejecting it as spam:
>
> “I’m looking to choose a graphics card for running AMBER. For cards that are not listed on the official Amber benchmark like the 2060, or 1070ti, has anybody been using these models? I assume it should definitely work, and a general benchmark found elsewhere should be a good estimate of relative performance-but I just want to ask about someone’s actual first-hand experience, with either a 1070Ti, 2060 or 2070, do they run AMBER properly?”
>
> Thanks,
> James
>
> Sent from my iPhone
>
>> On Dec 21, 2019, at 12:50 AM, MUHAMMAD KHATTAB FATHI KHATTAB <100030036.student.swin.edu.au<mailto:100030036.student.swin.edu.au<mailto:100030036.student.swin.edu.au%3cmailto:100030036.student.swin.edu.au>>> wrote:
>>
>> Dear All,
>>
>> As a beginner, I am wondering how to start using AMBER on supercomputer?
>> What are the required files? How to prepare them?
>> Regards,
>> Muhammad
>> _______________________________________________
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>
>
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Received on Sat Dec 21 2019 - 09:30:02 PST
