Amber安装

Amber 安装

下载Amber安装包

https://ambermd.org/index.php

Install pre-request

sudo apt install bc csh flex xorg-dev zlib1g-dev build-essential libbz2-dev patch cmake bison gfortran python

Amber AmberTools解压

tar xvfj AmberTools21.tar.bz2 # Ambertools are open source
tar xvfj Amber20.tar.bz2      # only when you have amber

编译安装

GPU版

cd amber20_src
./update_amber --upgrade
mkdir build-001
cd build-001
cmake ../ \
    -DCMAKE_INSTALL_PREFIX=~/Software/Amber20_cuda \
    -DCOMPILER=GNU  \
    -DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
    -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE

CPU版

cd amber20_src
./update_amber --upgrade
mkdir build-001
cd build-001
cmake ../ \
    -DCMAKE_INSTALL_PREFIX=~/Software/Amber20_CPU \
    -DCOMPILER=GNU  \
    -DMPI=FALSE  -DINSTALL_TESTS=TRUE \
    -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE

编译

make install -j 4 # 4 cores will be used, change accordingly

配置环境变量

source ~/Software/Amber20_cuda(cpu)/amber.sh 

测试

cd ~/Software/Amber20_cuda(cpu)
make test.cuda.serial
make test.serial