Amber Test Job

From UGP-Wiki

Amber is a molecular dynamics software package. in.md crd.md.23 and prmtop are input files to test Amber serial or parallel jobs.

in.md looks like this:

 cytosine in chloroform
 &cntrl
  irest  = 1, ntx    = 7,
  ntb    = 2, ntp    = 2, taup=0.2,
  ntt    = 1, tautp=0.2,
  nstlim = 10,
  dt     = 0.002, nrespa=1,
  ntpr   = 1, ntave=1000,
  temp0  = 300.,
  scee   = 1.2,
  ntf = 2, ntc = 2, tol=0.000005,
  vlimit=15.0,
 /

crd.md.23 looks like this:

1-methyl cytosine.                                                              
 1271  0.5420000E+04
   5.4352019  16.2705460  10.6228732   5.4627028  15.2477894  10.9987844
   4.5231658  15.1503616  11.5427311   6.3405717  15.2231882  11.6444171
   5.5797104  14.0809722  10.0273027   4.5821932  13.1399183  10.0403180
...(1270 data lines omitted)

prmtop looks like this:

1-methyl cytosine.                                                              
  1271    11   258   762   766   765    20    15     0     0  2830   252
   762   765    15    26    52    28    15     0     0     0     0     0
     0     0     0     1    16     0
HME1CME HME2HME3N1  C6  H6  C5  H5  C4  N4  H41 H42 N3  C2  O2  H   C   CL1 CL2 
CL3 H   C   CL1 CL2 CL3 H   C   CL1 CL2 CL3 H   C   CL1 CL2 CL3 H   C   CL1 CL2 
CL3 H   C   CL1 CL2 CL3 H   C   CL1 CL2 CL3 H   C   CL1 CL2 CL3 H   C   CL1 CL2 
CL3 H   C   CL1 CL2 CL3 H   C   CL1 CL2 CL3 H   C   CL1 CL2 CL3 H   C   CL1 CL2
...(2460 data lines omitted)

To test using this job:

1. Use the Data Manager to copy them to the cluster on which you will run Amber.
2. Select "Applications" under the "Job Services" tab.
3. Select Amber or Amber-Parallel under the cluster name from the frame on the left side of the page.
4. Fill in the Applications form as follows:
   1. Enter in the text field labeled "Arguments:".

      -O -i in.md -c crd.md.23 -p prmtop -o amber.out

   2. If in.md is not in your home directory, enter in the text field labeled "Directory:" either the full pathname of the directory containing cpmd.in or a path relatative to your home directory.
   3. Enter either 1 processor for serial, or many processors for parallel for the "Number of processors:".
   4. Click the "Submit Job" button.

The output file is called amber.out in the chosen directory.