Re: [AMBER] the command to make the sander running visible

From: Adrian Roitberg <roitberg.ufl.edu>
Date: Sun, 08 Apr 2012 10:37:06 -0400

if you really typed

$AMBERHOME/exe/sander -O -i polyAT_vac_md1_12Acut.in -o
polyAT_vac_md1_12Acut.out -c polyAT_vac_init_min.rst -p polyAT_vac.prmtop
-r polyAT_vac_md1_12Acut.rst -x polyAT_vac_md1_12Acut.mdcrd tail -f
polyAT_vac_md1_12Acut.out

then indeed, it is wrong.

everything after sander is READ by sander itself

tail is not something sander understands


Assuming you are running this interactively in your machine, then try

$AMBERHOME/exe/sander -O -i polyAT_vac_md1_12Acut.in -o
polyAT_vac_md1_12Acut.out -c polyAT_vac_init_min.rst -p polyAT_vac.prmtop
-r polyAT_vac_md1_12Acut.rst -x polyAT_vac_md1_12Acut.mdcrd &

note the & at the end

this sends it to background.

THEN you can type

tail -f polyAT_vac_md1_12Acut.out




On 4/8/12 10:28 AM, Aron Broom wrote:
> I'm not sure, but I suspect you can get it working by doing something like
> -o stdout
>
> Then instead of sending the output to the file, it will just print it on
> the screen. If you want both, I'm sure there is a way to get that to
> happen, but I'm not sure these are AMBER specific questions (at least in
> the way I'm answering it), but more linux shell questions.
>
> ~Aron
>
> On Sun, Apr 8, 2012 at 9:10 AM, Acoot Brett<acootbrett.yahoo.com> wrote:
>
>> Dear All,
>>
>> I have tried to use tail, but it does not work
>>
>> I use the following command, is anything wrong?
>> "$AMBERHOME/exe/sander -O -i polyAT_vac_md1_12Acut.in -o
>> polyAT_vac_md1_12Acut.out -c polyAT_vac_init_min.rst -p polyAT_vac.prmtop
>> -r polyAT_vac_md1_12Acut.rst -x polyAT_vac_md1_12Acut.mdcrd tail -f
>> polyAT_vac_md1_12Acut.out"
>>
>> It says tail cannot be recognized.
>>
>> I am looking forward to getting your reply on how to solve the problem.
>>
>> Cheers,
>>
>> Acoot
>>
>>
>> ----- Original Message -----
>> From: Acoot Brett<acootbrett.yahoo.com>
>> To: AMBER Mailing List<amber.ambermd.org>
>> Cc:
>> Sent: Sunday, 8 April 2012 10:13 PM
>> Subject: [AMBER] the command to make the sander running visible
>>
>> Dear All,
>>
>> As for the sander MD step usually takes a long time, it makes the computer
>> looks like dead.
>>
>> Will you please tell me the sander command to show the sander MD process
>> is on going, especially the sander command which indicates how much time
>> left to complete the on-going sander step?
>>
>> Cheers,
>>
>> Acoot
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
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>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>

-- 
                            Dr. Adrian E. Roitberg
                                  Professor
                Quantum Theory Project, Department of Chemistry
                            University of Florida
                              roitberg.ufl.edu
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Received on Sun Apr 08 2012 - 08:00:03 PDT
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