AMBER18 & AMBERTOOLS18 installation-Linux system

1. Prepare amber18 and ambertools18 compressed packages

Unzip the two tarballs in linux

-tar -xf Amber18.tar

tar -xf AmberTools.tar

Both files will be decompressed to the same Amber18 folder

2. Set environment variables

nano ~ / .bashrc Open the bashrc file

and add the installation path of

Amber18 export AMBERHOME = / home / liwen / amber18

export PATH = $ PATH: / home / soft / amber18 / bin

Exit save
source ~ / .bashrc activation

3. Run the configuration file

./configure --skip-python gnu It

should be noted here that the python version must be above 2.7. You can view detailed commands by viewing
./configure to indicate

that two files will be generated after running, one is amber.sh and one is amber .csh

Here we source the amber.sh file to correct the environment variable

source /home/liwen/amber18/amber.sh

Here we should pay attention to modify the command according to your own amber18 installation path
or directly add amber.sh to the ~ / .bashrc file to avoid source amber.sh file every time.

4. Compile and test

Make install

make test

test part can skip the

run after running antechamber command to see if amber is installed, if this command can be executed, it is installed,
if not, check the environment variables in ~ / .bashrc Path, and whether the amber.sh file was sourced before.

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Amber18 installation (non-root user)

installation method of the dynamic software Amber18. Although there are only a few steps, the process is quite
difficult, and it is easy to report errors during the installation.

Two installation packages

Amber18.tar.bz2 and AmberTools18.tar.bz2

Extract the two installation packages:

tar xjf Amber18.tar.bz2

tar xjf AmberTools18.tar.bz2

After the operation is completed, the amber18 directory will be generated in the directory
Then set environment variables and add in ~ / .bashrc

Finally source ~ / .bashrc

2. Configuration

Enter amber18, cd amber18

You can enter ./configure --full-help to see the command
explanation here .

Here you can see the choice of compiler, it is strongly recommended to use intel compilation (because I have
reported other errors). Moreover, if the Intel version is 12-17 , the 18 version will report an error. The following is
about python, it is best to have already installed python , otherwise during the configuration process, you will be
asked if you want to install minicanda, and there will be some unnecessary troubles and errors.

input the command:

./configure --with-python ~ / anaconda3 / bin / python intel

3. Compile
If there is no error in step 2, then there is basically no error in step 3.

command:

make install
This step may take 40 minutes. After compilation, amber.csh and amber.sh will be
generated in the directory.

4. Test
command:
make test
This step may take more than an hour.
https://blog.csdn.net/wzl1997/article/details/102708269

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Installation of Amber16 and AmberTools16 GPU accelerated version under CentOS 7

The AMBER molecular dynamics package was written by Peter A Kollman and
colleagues at the University of California San Francisco (UCSF). The program is
comprehensive and contains about 60 programs that work in coordination with each
other. It has now evolved to version 17. The AMBER function covers a wide variety of
biological molecules, including proteins, accounting and small drug molecules.

Hardware environment:

Hardware environment:
Compile dependencies

yum install gcc #install gcc

yum install g ++ #install g ++
yum install gfortran #install gfortran
yum install flex #install flex
yum install cmake #install cmake
yum install bzip2-devel
Compile and install Amber16 and AmberTools

tar xvjf AmberTools16.tar.bz2

tar xvjf Amber16.tar.bz2
cd amber16/

./configure --no-updates gnu

test -f /home/Aspirin/amber/amber16/amber.sh && source
/home/Aspirin/amber/amber16/amber.sh
make clean
make install

./configure -cuda -mpi --no-updates gnu

test -f /home/Aspirin/amber/amber16/amber.sh && source

/home/Aspirin/amber/amber16/amber.sh

make clean
make install
cd test
make test

Configure environment variables

gedit ~ /. bashrc #Open the bashrc file

#install amber16
export AMBERHOME=/home/aspirin/amber/amber16
export PATH=AMBERHOME/bin:$PATH
source /home/aspirin/amber/amber16/amber.sh

source ~ /.bashrc #source takes effect immediately

running result
for reference only!

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Ubuntu 18.04 LTS installation and configuration driver, CUDA9.1 and Amber18 &
AmberTools18

Table of Contents

Environment

2. Driver installation

2.1 Driver Download: https://www.nvidia.com/download/driverResults.aspx/132541/

2.2. Delete the original NVIDIA driver

2.3 disable nouveau

2.4. Query Your Graphics Card Model

2.5. Installation

2.6. Check if the installation is successful, command

3. CUDA9.1 installation

3.1 CUDA9.1 Download:

3.2 Run terminal input command to install in cuda download directory

3.3 Install the patch:

3.4 Setting the cuda environment variable

3.5 Verify that cuda is successfully installed

4. Amber18 & AmberTools18 installation

4.1 Installation environment dependencies

4.2 Extracting the installation package

4.3 Configuring environment variables

4.4 Compile Amber18

(Amber18's GPU supports CUDA version up to 9.2)

Environment
Hardware: GPU: Quadro P600
System: Ubuntu 18.04
2. Driver installation
2.1 Driver
Download: https://www.nvidia.com/download/driverResults.aspx/
132541/
2.2. Delete the original NVIDIA driver
sudo apt-get remove --purge nvidia*

2.3 disable nouveau

sudo vi /etc/modprobe.d/blacklist.conf

Add in the last line

blacklist nouneau
carried out

sudo update-initramfs -u

Restart

lsmod | grep nouveau # No output means disable takes effect, it must be executed after restart

2.4. Query Your Graphics Card Model

lshw -numeric -C display

Graphics: Quadro P600

2.5. Installation
sudo chmod a+x NVIDIA-Linux-x86_64-390.46.run
sh NVIDIA-Linux-x86_64-390.46.run

 Install only driver files, not OpenGL files. This parameter is the most important
 Don't check X service when installing driver
 Nouveau is not checked when installing the driver

2.6. Check if the installation is successful, command

nvidia-smi

3. CUDA9.1 installation
Ubuntu18.04By default GCC-7.3.0, because it is CUDA 9.1not supported GCC-7, you need to install a lower
version 5or <= 6.3.0set it as the default version.
3.1 CUDA9.1 Download:
https://developer.nvidia.com/cuda-91-download-archive?target_os=Linux
3.2 Run terminal input command to install in cuda download
directory
sudo sh cuda_9.1.85_387.26_linux.run

After reading the agreement, select accept, in addition to installing the nvidia driver and installing
NVIDIA_CUDA-9.1_Samples, select Yes, and then select all to successfully install it;

3.3 Install the patch:

sudo sh cuda_9.1.85.1_linux.run
3.4 Setting the cuda environment variable
Use: vim ~ / .bashrc command to open ~ / .bashrc file, write the following content

#CUDA9.1
export CUDA_HOME=/usr/local/cuda-9.1
export PATH=/usr/local/cuda-9.1/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-9.1/lib64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH="/usr/local/cuda-9.1/lib:${LD_LIBRARY_PATH}"

After saving and exiting, run: source ~ / .bashrc

3.5 Verify that cuda is successfully installed

cd /usr/local/cuda-9.1/samples/1_Utilities/deviceQuery
sudo make
./deviceQuery

Finally it appears: Result = PASS. deviceQuery, CUDA Driver = CUDART, CUDA Driver
Version = 10.0, CUDA Runtime Version = 9.1, NumDevs = 1 Result = PASS

4. Amber18 & AmberTools18 installation

4.1 Installation environment dependencies
gcc, g ++, gfortran version must be lower than 6.0

apt-get install bison bc csh flex gfortran g++ xorg-dev zlib1g-dev libbz2-dev patch
python

4.2 Extracting the installation package

tar jxvf AmberTools18.tar.bz2
tar jxvf Amber18.tar.bz2

4.3 Configuring environment variables

~ /.bashrc added

vi ~ /.bashrc #Open the bashrc file

#Amber18
test -f /opt/amber18/amber.sh && source /opt/amber18/amber.sh
export AMBERHOME=/opt/amber18
export CUDA_HOME=/usr/local/cuda
export PATH=$PATH:$CUDA_HOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib64

source ~ / .bashrc #source takes effect immediately

4.4 Compile Amber18

Compile the serial version

cd amber18

./configure --no-updates --with-python /usr/anaconda3/bin/python gnu

test -f /opt/amber18/amber.sh && source /opt/amber18/amber.sh
make clean
make install -j 25
make test

Compile parallel version

cd amber18

./configure --no-updates --with-python /usr/anaconda3/bin/python -mpi gnu

test -f /opt/amber18/amber.sh && source /opt/amber18/amber.sh
make clean
make install -j 25
make test

Compile GPU version

cd amber18

./configure --no-updates --with-python /usr/anaconda3/bin/python -cuda gnu

test -f /opt/amber18/amber.sh && source /opt/amber18/amber.sh
make install -j 25

Parallel

./configure --no-updates --with-python /usr/anaconda3/bin/python -cuda -mpi gnu

test -f /opt/amber18/amber.sh && source /opt/amber18/amber.sh
make install -j 25

make test
https://blog.csdn.net/u012325865/article/details/103456040

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Gromacs 5.1.4 GPU accelerated version installation under CentOS7

GROMACS is a calculation engine for molecular dynamics simulation and energy

minimization. Molecular dynamics simulation and energy minimization are two of many
technologies in the field of computational chemistry and molecular modeling.
Computational chemistry is the application of computational technology in chemistry, It
covers the quantum mechanics of molecules to the dynamics of complex macromolecular
aggregates. Molecular modeling is a general method for describing complex chemical
systems with practical atomic models, the purpose of which is to understand and predict
matter based on detailed knowledge at the atomic scale Macroscopic properties. Often,
molecular modeling is used to design new materials, because in the process, accurate
predictions of the physical properties of actual systems are required.

Hardware environment:

Install dependencies
Kernel dependencies
yum install kernel-headers
yum install kernel-devel

yum install kernel-devel-kernel-devel-3.10.0-514.21.1.el7.x86_64

Compile dependencies
yum install gcc
yum install gcc-c++
yum install gcc-gfortran
yum install cmake
yum install blas-devel
yum install lapack-devel
yum install boost-devel
yum install libxml2-devel
yum install libpng-devel
yum -y install doxygen
Compile and install Gromacs-5.1.4

tar zxvf gromacs-5.1.4.tar.gz

cd gromacs-5.1.4
mkdir build
cd build

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/opt/gmx

make -j 12 #Computer 14 cores, select 12

make install

Configure environment variables

gedit ~ / .bashrc #Open bashrc

source /opt/gmx5/bin/GMXRC #environment variable

source ~ /.bashrc #source takes effect immediately

running result
https://blog.csdn.net/u012325865/article/details/73028480
cuda ins
https://blog.csdn.net/u012325865/article/details/73034018