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howto:amber [2016/03/30 11:56]
kgovender
howto:amber [2018/09/13 15:38] (current)
kgovender
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 When running jobs for either AMBER12 or AMBER14 use the easy setup and submission scripts provided on the login node. When running jobs for either AMBER12 or AMBER14 use the easy setup and submission scripts provided on the login node.
-Just execute **qamber_12** ​or **qamber_14**.+Just execute **qamber_12****qamber_14** or **qamber_18**.
 Examples of what the scripts look like are provided below. Examples of what the scripts look like are provided below.
  
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   Do you wish to submit job to cluster (y/n)   Do you wish to submit job to cluster (y/n)
   y   y
 +  ​
 +====== AMBER18 on GPU ======
 +
 +** //Please note that you need to first be added to the gpu_1 queue before you can submit jobs to the GPU cluster// **
 +
 +Execute **qamber_18_gpu** on login node and follow the prompts.
 +Examples of script execution are provided below.
 +
 +                    EXAMPLE1
 +  Enter research programme name
 +  CHEM01
 +  Enter input file (with .in extension)
 +  test.in
 +  Enter parameter and topology file
 +  prmtop
 +  Enter coordinate file
 +  inpcrd
 +  Enter total walltime (hour:​minute)
 +  2:00
 +  Enter email address
 +  testing@gmail.com
 +  Generated pbs file for test
 +  Do you wish to submit job to cluster (y/n)
 +  y
 +
 +   
 +
 +    EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
 +  Enter research programme name
 +  CHEM01
 +  Enter input file (with .in extension)
 +  test.in
 +  Enter parameter and topology file
 +  ​
 +  Enter coordinate file
 +  ​
 +  Enter total walltime (hour:​minute)
 +  ​
 +  Enter email address
 +  testing@gmail.com
 +  Generated pbs file for test
 +  Do you wish to submit job to cluster (y/n)
 +  y
 +
/var/www/wiki/data/pages/howto/amber.txt · Last modified: 2018/09/13 15:38 by kgovender