# AMBER

AMBER is a highly parallized suite of biomolecular simulation programs which use MPI and OpenMP on CPUs or CUDA (in combination with MPI) to run on GPUs.

Amber is distributed in two parts: AmberTools and Amber. Amber is a package of molecular simulation programs, AmberTools  contains a collection of useful software to analyze and modify MD data. You can find a comprehensive manual here.

## Examples

### AmberTools on CPU with MPI: MMPBSA.py.MPI

The following example runs MMPBSA.py.MPI on 20 identical CPUs. Each of the called Sander jobs (used for surface and energy calculation)  may take up to 4G of RAM - for bigger systems this has to be adjusted. The code below runs a 'stability calculation' for a single system. For a comprehensive overview the the AMBER18 manual.

Keep in mind, that MMPBSA calculations are more demanding in terms of memory than MMGBSA jobs.

MMPBSA_py_MPI.pbs
```#!/bin/bash

#PBS -l walltime=XX:YY:ZZ
#PBS -l select=20:ncpus=1:mpiprocs=1:mem=4G
#PBS -l place=group=arch
#PBS -r n
#PBS -N Job Name
#PBS -A Project Name

# input files
INFILE=MMPBSA.infile
EOFILE=Output.dat
PRMTOP=Topology.prmtop
TRAJ=Trajectory.nc

# go to work dir
cd $PBS_O_WORKDIR # def executable MPI_EXE=`which MMPBSA.py.MPI` # generate log file LOGFILE=$PBS_O_WORKDIR/$PBS_JOBNAME"."$PBS_JOBID".log"
echo "$PBS_JOBID ($PBS_JOBNAME) @ `hostname` at `date` in "$PBS_O_WORKDIR" START" >$LOGFILE
echo "`date +"%d.%m.%Y-%T"`" >> $LOGFILE echo >>$LOGFILE
echo "GLOBAL PARAMETERS">> $LOGFILE echo "---------------------------" >>$LOGFILE
echo "Node       : "$HOSTNAME >>$LOGFILE
echo "Arch       : "$ARCH >>$LOGFILE
echo "---------------------------" >> $LOGFILE echo "RunDir : "$PBS_O_WORKDIR >> $LOGFILE # MPICPUS=$(cat $PBS_NODEFILE | wc -l) echo "# MPI CPUs:${MPICPUS}" >> $LOGFILE mpirun$MPI_EXE -i $INFILE -eo$EOFILE -cp $PRMTOP -y$TRAJ  >>$LOGFILE qstat -f$PBS_JOBID >> $LOGFILE echo "$PBS_JOBID ($PBS_JOBNAME) @ `hostname` at `date` in "$RUNDIR" END" >> $LOGFILE echo "`date +"%d.%m.%Y-%T"`" >>$LOGFILE```
Short-Info
AMBER
CategoryMD-Simulations
UsageCPU or GPU
Module-Versions
AMBER12-18