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fireball_18.02_ambertools_17

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fireball_18.02_ambertools_17 [2018/02/15 12:27]
jesus created
fireball_18.02_ambertools_17 [2018/03/22 19:21] (current)
Line 1: Line 1:
-  * EXTERN+====== Fireball & Amber with EXTERN ​(mpi) ====== 
  
   mkdir fireball   mkdir fireball
Line 8: Line 9:
  
 change in Makefile: change in Makefile:
-MACHINE = your options +  * MACHINE = your options 
-PARALLEL = MPI +  ​* ​PARALLEL = MPI 
-METHOD = SCALAPACK+  ​* ​METHOD = SCALAPACK 
 + 
   ​   ​
   make server_amber   make server_amber
   ​   ​
  
-  ​Download AmberTools17.tar+Download AmberTools17.tar ​from http://​ambermd.org/​ 
   tar -xvf AmberTools17.tar   tar -xvf AmberTools17.tar
   cd amber16   cd amber16
Line 26: Line 30:
   cp $FIREBALLHOME/​progs/​QMMM/​qm2/​qm2_extern_fb_module.F90 $AMBERHOME/​AmberTools/​src/​sander/​   cp $FIREBALLHOME/​progs/​QMMM/​qm2/​qm2_extern_fb_module.F90 $AMBERHOME/​AmberTools/​src/​sander/​
   cp $FIREBALLHOME/​progs/​QMMM/​qm2/​depend $AMBERHOME/​AmberTools/​src/​sander/​   cp $FIREBALLHOME/​progs/​QMMM/​qm2/​depend $AMBERHOME/​AmberTools/​src/​sander/​
-  cp $FIREBALLHOME/​progs/​QMMM/​qm2/​Makefile.sander.server $AMBERHOME/​AmberTools/​src/​sander/​+  cp $FIREBALLHOME/​progs/​QMMM/​qm2/​Makefile.sander.server $AMBERHOME/​AmberTools/​src/​sander/​Makefile
   cd $AMBERHOME   cd $AMBERHOME
   ./configure -intelmpi intel   ./configure -intelmpi intel
   make   make
 +
 +====== Run an Example ======
  
  
   cd $FIREBALLHOME/​progs/​QMMM/​thym_qmmm   cd $FIREBALLHOME/​progs/​QMMM/​thym_qmmm
 +  wget http://​fireball.ftmc.uam.es/​Fdata_HCNO.tar.gz
 +  tar -xvf  Fdata_HCNO.tar.gz ​
   mpdboot   mpdboot
-  mpiexec -n 1 -env I_MPI_DEVICE sock $FIREBALLHOME/​progsfireball_server +  mpiexec -n 1 -env I_MPI_DEVICE sock $FIREBALLHOME/​progs/​fireball_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_17.1518694051.txt.gz · Last modified: 2018/02/15 12:27 (external edit)