fireball_18.02_ambertools_17
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fireball_18.02_ambertools_17 [2018/02/15 12:27] jesus |
fireball_18.02_ambertools_17 [2018/02/15 12:35] jesus |
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| - | * EXTERN | + | ====== Fireball & Amber with EXTERN (mpi) ====== |
| mkdir fireball | mkdir fireball | ||
| Line 8: | Line 9: | ||
| change in Makefile: | change in Makefile: | ||
| + | * MACHINE = your options | ||
| + | * PARALLEL = MPI | ||
| + | * METHOD = SCALAPACK | ||
| - | MACHINE = your options | ||
| - | |||
| - | PARALLEL = MPI | ||
| - | |||
| - | METHOD = SCALAPACK | ||
| | | ||
| Line 19: | Line 18: | ||
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| - | Download AmberTools17.tar | + | Download AmberTools17.tar from http://ambermd.org/ |
| tar -xvf AmberTools17.tar | tar -xvf AmberTools17.tar | ||
| cd amber16 | cd amber16 | ||
| Line 34: | Line 34: | ||
| ./configure -intelmpi intel | ./configure -intelmpi intel | ||
| make | make | ||
| + | |||
| + | ====== Run an Example ====== | ||
| Line 39: | Line 41: | ||
| mpdboot | mpdboot | ||
| mpiexec -n 1 -env I_MPI_DEVICE sock $FIREBALLHOME/progsfireball_server | mpiexec -n 1 -env I_MPI_DEVICE sock $FIREBALLHOME/progsfireball_server | ||
| - | mpiexec -n 1 -env I_MPI_DEVICE sock $AMBERHOME/bin/sander.MPI -O -i amber.in -o outmd -p thym_qmmm.prmtop -c | + | mpiexec -n 1 -env I_MPI_DEVICE sock $AMBERHOME/bin/sander.MPI -O -i amber.in -o outmd -p thym_qmmm.prmtop -c thym_qmmm.inpcrd -x answer.mdcrd -r answer.rst |
| - | thym_qmmm.inpcrd -x answer.mdcrd -r answer.rst | + | |
| + | |||
fireball_18.02_ambertools_17.txt · Last modified: 2018/03/22 19:21 (external edit)
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