Centos7.9 部署分子动力学相关软件_centos7.9 没有可用软件包 devtoolset-11-CSDN博客

本文链接：https://blog.csdn.net/weixin_44217077/article/details/143140682

Centos7.9 部署分子动力学相关软件

一. Centos7.9 基础工具安装及一些环境配置

1.1 Centos DNS配置

在配置文件 /etc/resolv.conf 中添加

nameserver 8.8.8.8
nameserver 114.114.114.114

验证，ping一下百度和阿里的域名
可以ping通，配置完成

1.2 yum 换源

编写脚本 auto_aliyun.sh

#!/bin/bash

# 备份官方的原yum源的配置
mv /etc/yum.repos.d/CentOS-Base.repo /etc/yum.repos.d/CentOS-Base.repo.backup
# 下载Centos-7.repo文件,或者curl -o /etc/yum.repos.d/CentOS-Base.repo http://mirrors.aliyun.com/repo/Centos-7.repo，取决于你是否有wget的命令
wget -O /etc/yum.repos.d/CentOS-Base.repo http://mirrors.aliyun.com/repo/Centos-7.repo
# 清除yum缓存
yum clean all
# 缓存本地yum源
yum makecache

给执行权限并运行

chmod 777  auto_aliyun.sh & ./ auto_aliyun.sh

1.3 Centos7 yum只下载不安装, 离线安装

下载命令
```
 yumdownloader xxx
```
安装命令
```
rpm -ivh xxx.rpm
```

1.4 Centos7 安装 cmake3

执行命令

yum install -y epel-release
yum install -y cmake3

验证

[root@FST-SJKS-01 build]# cmake3 --version 
cmake3 version 3.17.5

CMake suite maintained and supported by Kitware (kitware.com/cmake).

1.5 其它基本工具安装

执行命令, 两个命令，执行就完了

sudo yum install flex tcsh zlib-devel \
     bzip2-devel libXt-devel libXext-devel libXdmcp-devel \
     tkinter openmpi openmpi-devel perl perl-ExtUtils-MakeMaker \
     patch bison boost-devel
	 
sudo yum install python-devel tkinter python-pmw glew-devel \
  freeglut-devel libpng-devel freetype-devel libxml2-devel glm-devel

二. Centos7.9 使用scl+devtoolse-11 升级gcc

安装scl （先解决yum源的问题）

yum install centos-release-scl centos-release-scl-rh

安装完成后会默认在 /etc/yum.repos.d 下生成 2 个 repo 源文件，如果没有生成，自己写

#CentOS-SCLo-rh.repo
#
# Please see http://wiki.centos.org/SpecialInterestGroup/SCLo for more
# information

[centos-sclo-rh]
name=CentOS-7 - SCLo rh
baseurl=https://mirrors.aliyun.com/centos/7/sclo/x86_64/rh/ # 注意：这里推荐改成国内的源
# mirrorlist=http://mirrorlist.centos.org?arch=$basearch&release=7&repo=sclo-rh
gpgcheck=0
enabled=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo


[centos-sclo-rh-testing]
name=CentOS-7 - SCLo rh Testing
baseurl=http://buildlogs.centos.org/centos/7/sclo/$basearch/rh/
gpgcheck=0
enabled=0
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo

[centos-sclo-rh-source]
name=CentOS-7 - SCLo rh Sources
baseurl=http://vault.centos.org/centos/7/sclo/Source/rh/
gpgcheck=1
enabled=0
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo

[centos-sclo-rh-debuginfo]
name=CentOS-7 - SCLo rh Debuginfo
baseurl=http://debuginfo.centos.org/centos/7/sclo/$basearch/
gpgcheck=1
enabled=0
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo

#CenntOS-SCLo-sclo.repo
#
# Please see http://wiki.centos.org/SpecialInterestGroup/SCLo for more
# information

[centos-sclo-sclo]
name=CentOS-7 - SCLo sclo
baseurl=https://mirrors.aliyun.com/centos/7/sclo/x86_64/sclo/ # 注意：这里推荐改成国内的源
# mirrorlist=http://mirrorlist.centos.org?arch=$basearch&release=7&repo=sclo-sclo
gpgcheck=0
enabled=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo

[centos-sclo-sclo-testing]
name=CentOS-7 - SCLo sclo Testing
baseurl=http://buildlogs.centos.org/centos/7/sclo/$basearch/sclo/
gpgcheck=0
enabled=0
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo

[centos-sclo-sclo-source]
name=CentOS-7 - SCLo sclo Sources
baseurl=http://vault.centos.org/centos/7/sclo/Source/sclo/
gpgcheck=1
enabled=0
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo

[centos-sclo-sclo-debuginfo]
name=CentOS-7 - SCLo sclo Debuginfo
baseurl=http://debuginfo.centos.org/centos/7/sclo/$basearch/
gpgcheck=1
enabled=0
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-SIG-SCLo

更新 yum 源的缓存
```
yum clean all
yum makecache
```

安装 Devtoolset

查看支持的版本

yum search devtoolset --enablerepo='centos-sclo-rh'

因为笔者需要的是gcc 11 ，所以可以

 yum search devtoolset --enablerepo='centos-sclo-rh' | grep devtoolset-11

请添加图片描述

安装

yum install devtoolset-11-gcc.x86_64  devtoolset-11-gcc-c++.x86_64  devtoolset-11-gcc-gfortran.x86_64 devtoolset-11-gcc-plugin-devel.x86_64

scl 基本使用

# 查看通过 scl 安装了哪些软件
scl -l
scl --list

请添加图片描述
使用scl之前 gcc g++ gforchan 的版本都是 4.8.5

当前命令行使能哪个scl的软件

 scl enable devtoolset-11 bash
 # 或者使用 
 source /opt/rh/devtoolset-11/enable  # 如果之后每个终端都要使用这个版本的软件可以将这行加到 ~/.bashrc 中

请添加图片描述

可以看到执行完 scl enable devtoolset-11 bash 命令后， gcc g++ gforchan的版本变成了 11.2.1

三. 安装fftw-3.3.8 (gromacs-2018.8的依赖)

下载 http://www.fftw.org/fftw-3.3.8.tar.gz ，解压后进入目录执行

./configure --prefix=/sob/fftw338 --enable-sse2 --enable-avx --enable-float --enable-shared

然后进一步运行
```
make -j install
```
最后的效果

四. 安装gromacs

4.1 gromacs-2018.8

下载 http://ftp.gromacs.org/pub/gromacs/gromacs-2018.8.tar.gz ，解压后进入目录

依次执行

mkdir build
cd build
export CMAKE_PREFIX_PATH=/sob/fftw338
cmake3 .. -DCMAKE_INSTALL_PREFIX=/sob/gmx2018.8

编译安装
```
make install -j
```

报错
请添加图片描述

In file included from /root/Andrea/gromacs-2018.8/src/gromacs/utility/arrayref.h:54,
                 from /root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:55:
/root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp: In function ‘gmx_int64_t gmx::{anonymous}::calcCheckCoveringInterval(const gmx::AwhParams&, const std::vector<gmx::DimParams>&, const std::vector<gmx::GridAxis>&)’:
/root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:137:62: error: ‘numeric_limits’ is not a member of ‘std’
  137 |         GMX_RELEASE_ASSERT(gridAxis[d].length()/sigma < std::numeric_limits<int>::max(), "The axis length in units of sigma should fit in an int");
      |                                                              ^~~~~~~~~~~~~~
/root/Andrea/gromacs-2018.8/src/gromacs/utility/gmxassert.h:67:15: note: in definition of macro ‘GMX_RELEASE_ASSERT’
   67 |     ((void) ((condition) ? (void)0 : \
      |               ^~~~~~~~~
/root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:137:77: error: expected primary-expression before ‘int’
  137 |         GMX_RELEASE_ASSERT(gridAxis[d].length()/sigma < std::numeric_limits<int>::max(), "The axis length in units of sigma should fit in an int");
      |                                                                             ^~~
/root/Andrea/gromacs-2018.8/src/gromacs/utility/gmxassert.h:67:15: note: in definition of macro ‘GMX_RELEASE_ASSERT’
   67 |     ((void) ((condition) ? (void)0 : \
      |               ^~~~~~~~~
/root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:137:77: error: expected ‘)’ before ‘int’
  137 |         GMX_RELEASE_ASSERT(gridAxis[d].length()/sigma < std::numeric_limits<int>::max(), "The axis length in units of sigma should fit in an int");
      |                                                                             ^~~
/root/Andrea/gromacs-2018.8/src/gromacs/utility/gmxassert.h:67:15: note: in definition of macro ‘GMX_RELEASE_ASSERT’
   67 |     ((void) ((condition) ? (void)0 : \
      |               ^~~~~~~~~
/root/Andrea/gromacs-2018.8/src/gromacs/utility/gmxassert.h:67:14: note: to match this ‘(’
   67 |     ((void) ((condition) ? (void)0 : \
      |              ^
/root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:137:9: note: in expansion of macro ‘GMX_RELEASE_ASSERT’
  137 |         GMX_RELEASE_ASSERT(gridAxis[d].length()/sigma < std::numeric_limits<int>::max(), "The axis length in units of sigma should fit in an int");
      |         ^~~~~~~~~~~~~~~~~~
/root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:137:147: error: expected ‘)’ before ‘;’ token
  137 |         GMX_RELEASE_ASSERT(gridAxis[d].length()/sigma < std::numeric_limits<int>::max(), "The axis length in units of sigma should fit in an int");
      |                                                                                                                                                   ^
In file included from /root/Andrea/gromacs-2018.8/src/gromacs/utility/arrayref.h:54,
                 from /root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:55:
/root/Andrea/gromacs-2018.8/src/gromacs/utility/gmxassert.h:67:13: note: to match this ‘(’
   67 |     ((void) ((condition) ? (void)0 : \
      |             ^
/root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:137:9: note: in expansion of macro ‘GMX_RELEASE_ASSERT’
  137 |         GMX_RELEASE_ASSERT(gridAxis[d].length()/sigma < std::numeric_limits<int>::max(), "The axis length in units of sigma should fit in an int");
      |         ^~~~~~~~~~~~~~~~~~
/root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:137:147: error: expected ‘)’ before ‘;’ token
  137 |         GMX_RELEASE_ASSERT(gridAxis[d].length()/sigma < std::numeric_limits<int>::max(), "The axis length in units of sigma should fit in an int");
      |                                                                                                                                                   ^
In file included from /root/Andrea/gromacs-2018.8/src/gromacs/utility/arrayref.h:54,
                 from /root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:55:
/root/Andrea/gromacs-2018.8/src/gromacs/utility/gmxassert.h:67:5: note: to match this ‘(’
   67 |     ((void) ((condition) ? (void)0 : \
      |     ^
/root/Andrea/gromacs-2018.8/src/gromacs/awh/biasparams.cpp:137:9: note: in expansion of macro ‘GMX_RELEASE_ASSERT’
  137 |         GMX_RELEASE_ASSERT(gridAxis[d].length()/sigma < std::numeric_limits<int>::max(), "The axis length in units of sigma should fit in an int");
      |         ^~~~~~~~~~~~~~~~~~

解决方法

添加 #include <limits> 到 
src/gromacs/awh/biasparams.cpp 和 
src/gromacs/mdlib/minimize.cpp 两个文件的顶部

添加后，重新编译安装
```
make install -j
```
安装好后
验证安装效果
在.bashrc中添加命令
```
source /sob/gmx2018.8/bin/GMXRC
```
重新打开终端，执行
```
gmx -version 
```
出现版本信息，表明安装部署成功

4.2 gromacs-2022.6

依赖包括如下内容

gcc-8及以上、g++-8及以上、make 4及以上、cuda（根据自己的gpu选择版本）

需要更新gcc以及cmake ，笔者使用的是 scl + devtoolse11 ，直接安装所有的 devtoolset-11 中的软件

yum install devtoolset-11.x86_64 devtoolset-11-runtime.x86_64 devtoolset-11-annobin-annocheck.x86_64 devtoolset-11-annobin-docs.noarch devtoolset-11-annobin-plugin-gcc.x86_64 devtoolset-11-binutils.x86_64 devtoolset-11-binutils-devel.x86_64 devtoolset-11-build.x86_64 devtoolset-11-dwz.x86_64 devtoolset-11-dyninst.x86_64 devtoolset-11-dyninst-devel.x86_64 devtoolset-11-dyninst-doc.x86_64 devtoolset-11-dyninst-static.x86_64 devtoolset-11-dyninst-testsuite.x86_64 devtoolset-11-elfutils.x86_64 devtoolset-11-elfutils-debuginfod.x86_64 devtoolset-11-elfutils-debuginfod-client.x86_64 devtoolset-11-elfutils-debuginfod-client-devel.x86_64 devtoolset-11-elfutils-devel.x86_64 devtoolset-11-elfutils-libelf.x86_64 devtoolset-11-elfutils-libelf-devel.x86_64 devtoolset-11-elfutils-libs.x86_64 devtoolset-11-gcc.x86_64 devtoolset-11-gcc-c++.x86_64 devtoolset-11-gcc-gdb-plugin.x86_64 devtoolset-11-gcc-gfortran.x86_64 devtoolset-11-gcc-plugin-devel.x86_64 devtoolset-11-gdb.x86_64 devtoolset-11-gdb-doc.noarch devtoolset-11-gdb-gdbserver.x86_64 devtoolset-11-libasan-devel.x86_64 devtoolset-11-libatomic-devel.x86_64 devtoolset-11-libgccjit.x86_64 devtoolset-11-libgccjit-devel.x86_64 devtoolset-11-libgccjit-docs.x86_64 devtoolset-11-libitm-devel.x86_64 devtoolset-11-liblsan-devel.x86_64 devtoolset-11-libquadmath-devel.x86_64 devtoolset-11-libstdc++-devel.x86_64 devtoolset-11-libstdc++-docs.x86_64 devtoolset-11-libtsan-devel.x86_64 devtoolset-11-libubsan-devel.x86_64 devtoolset-11-ltrace.x86_64 devtoolset-11-make.x86_64 devtoolset-11-make-devel.x86_64 devtoolset-11-memstomp.x86_64 devtoolset-11-oprofile.x86_64 devtoolset-11-oprofile-devel.x86_64 devtoolset-11-oprofile-jit.x86_64 devtoolset-11-perftools.x86_64 devtoolset-11-strace.x86_64 devtoolset-11-systemtap.x86_64 devtoolset-11-systemtap-client.x86_64 devtoolset-11-systemtap-devel.x86_64 devtoolset-11-systemtap-initscript.x86_64 devtoolset-11-systemtap-runtime.x86_64 devtoolset-11-systemtap-sdt-devel.x86_64 devtoolset-11-systemtap-server.x86_64 devtoolset-11-systemtap-testsuite.x86_64 devtoolset-11-toolchain.x86_64 devtoolset-11-valgrind.x86_64 devtoolset-11-valgrind-devel.x86_64 devtoolset-11.x86_64 devtoolset-11-runtime.x86_64 devtoolset-11-annobin-annocheck.x86_64 devtoolset-11-annobin-docs.noarch devtoolset-11-annobin-plugin-gcc.x86_64 devtoolset-11-binutils.x86_64 devtoolset-11-binutils-devel.x86_64 devtoolset-11-build.x86_64 devtoolset-11-dwz.x86_64 devtoolset-11-dyninst.x86_64 devtoolset-11-dyninst-devel.x86_64 devtoolset-11-dyninst-doc.x86_64 devtoolset-11-dyninst-static.x86_64 devtoolset-11-dyninst-testsuite.x86_64 devtoolset-11-elfutils.x86_64 devtoolset-11-elfutils-debuginfod.x86_64 devtoolset-11-elfutils-debuginfod-client.x86_64 devtoolset-11-elfutils-debuginfod-client-devel.x86_64 devtoolset-11-elfutils-devel.x86_64 devtoolset-11-elfutils-libelf.x86_64 devtoolset-11-elfutils-libelf-devel.x86_64 devtoolset-11-elfutils-libs.x86_64

安装cuda (笔者使用的环境cuda版本为12.4，不是自己安装的(●ˇ∀ˇ●)，cuda12.4的安装过程请参考其它博主吧 ,ԾㅂԾ, )，版本信息显示如下
通过命令查看 cuda 的安装命令
```
$ which nvcc
/usr/local/cuda/bin/nvcc
```
上面的 /usr/local/cuda/ 就是同事部署的位置

下载 gromacs-2022.6.tar.gz

wget https://ftp.gromacs.org/gromacs/gromacs-2022.6.tar.gz

解压并进入目录

tar xvf gromacs-2022.6.tar.gz
cd gromacs-2022.6/
mkdir build 
cd build

切换scl
```
scl enable devtoolset-11 bash
```
检查 gcc（不低于8）、g++（不低于8）、 make（不低于4）是不是高版本的，

在build目录中执行 cmake 命令

cmake3 ..  -DCMAEK_INSTALL_PREFIX=/opt/gromacs-2022 -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-12.4/ -DGMX_BUILD_OWN_FFTW=ON

生成makefile等文件后，编译

make 
make check
sudo make install 
source /opt/gromacs-2022/bin/GMXRC  #建议这句加到 ~/.bashrc 中

查看版本信息
```
gmx --version 
```

五. 安装MiniConda 以及源的配置

下载安装脚本

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

执行安装

chmod 777 Miniconda3-latest-Linux-x86_64.sh 
sudo ./Miniconda3-latest-Linux-x86_64.sh

一路next，选yes
执行
```
 source ~/.bashrc 
```

修改 ~/.condarc ，亲测有效的源（20241022）

annels:
  - defaults
show_channel_urls: true
default_channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2
custom_channels:
  conda-forge: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  msys2: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  bioconda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  menpo: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  pytorch: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  pytorch-lts: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
  simpleitk: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud
auto_activate_base: false   #修改默认不进入base环境

六. 安装AmberTools23

运行以下命令

#创建一个新的 conda “环境”
conda create --name AmberTools23   
# 切换 conda 环境
conda activate AmberTools23
# 安装
conda install -c conda-forge ambertools=23
# 更新
conda update -c conda-forge ambertools
# 验证 antechamber 运行
(base) [root@localhost Andrea]# conda activate AmberTools23
(AmberTools23) [root@localhost Andrea]# antechamber 

Welcome to antechamber 22.0: molecular input file processor.

Usage: antechamber -i     input file name
                   -fi    input file format
                   -o     output file name
                   -fo    output file format
                   -c     charge method
                   -cf    charge file name
                   -nc    net molecular charge (int)
                   -a     additional file name
                   -fa    additional file format
                   -ao    additional file operation
                          crd   : only read in coordinate
                          crg   : only read in charge
                          radius: only read in radius
                          name  : only read in atom name
                          type  : only read in atom type
                          bond  : only read in bond type 
                   -m     multiplicity (2S+1), default is 1
                   -rn    residue name, overrides input file, default is MOL
                   -rf    residue toplogy file name in prep input file,
                          default is molecule.res
                   -ch    check file name for gaussian, default is 'molecule'
                   -ek    mopac or sqm keyword, inside quotes; overwrites previous ones
                   -gk    gaussian job keyword, inside quotes, is ignored when both -gopt and -gsp are used
                   -gopt  gaussian job keyword for optimization, inside quotes
                   -gsp   gaussian job keyword for single point calculation, inside quotes
                   -gm    gaussian memory keyword, inside quotes, such as "%mem=1000MB"
                   -gn    gaussian number of processors keyword, inside quotes, such as "%nproc=8"
                   -gdsk  gaussian maximum disk usage keyword, inside quotes, such as "%maxdisk=50GB"
                   -gv    add keyword to generate gesp file (for Gaussian 09 only)
                          1    : yes
                          0    : no, the default
                   -ge    gaussian esp file generated by iop(6/50=1), default is g09.gesp
                   -tor   torsional angle list, inside a pair of quotes, such as "1-2-3-4:0,5-6-7-8"
                          ':1' or ':0' indicates the torsional angle is frozen or not
                   -df    am1-bcc precharge flag, 2 - use sqm(default); 0 - use mopac
                   -at    atom type
                          gaff : the default
                          gaff2: for gaff2 (beta-version)
                          amber: for PARM94/99/99SB
                          bcc  : bcc 
                          sybyl: sybyl 
                   -du    fix duplicate atom names: yes(y)[default] or no(n)
                   -bk    component/block Id, for ccif
                   -an    adjust atom names: yes(y) or no(n)
                          the default is 'y' for 'mol2' and 'ac' and 'n' for the other formats 
                   -j     atom type and bond type prediction index, default is 4 
                          0    : no assignment
                          1    : atom type 
                          2    : full  bond types 
                          3    : part  bond types 
                          4    : atom and full bond type 
                          5    : atom and part bond type 
                   -s     status information: 0(brief), 1(default) or 2(verbose)
                   -eq    equalizing atomic charge, default is 1 for '-c resp' and '-c bcc' and 0 for the other charge methods 
                          0    : no use
                          1    : by atomic paths 
                          2    : by atomic paths and structural information, i.e. E/Z configurations 
                   -pf    remove intermediate files: yes(y) or no(n)[default]
                   -pl    maximum path length to determin equivalence of atomic charges for resp and bcc,
                          the smaller the value, the faster the algorithm, default is -1 (use full length),
                          set this parameter to 10 to 30 if your molecule is big (# atoms >= 100)
                   -seq   atomic sequence order changable: yes(y)[default] or no(n)
                   -dr    acdoctor mode: yes(y)[default] or no(n)
                   -i -o -fi and -fo must appear; others are optional
                   Use 'antechamber -L' to list the supported file formats and charge methods

七. 安装VMD

下载vmd安装包

wget https://www.ks.uiuc.edu/Research/vmd/alpha/vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl.tar.gz

解压

tar xvf vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl.tar.gz

进入解压目录
```
cd vmd-1.9.4a55
```
执行 configure
```
sudo ./configure
```
编译
```
sudo make install
```

终端输入vmd启动

su root
conda activate AmberTools23 # 切换到自己的conda环境
vmd xxx.pdb

请添加图片描述

vmd的配置
```
vi ~/.vmdrc
```
添加命令
```
user add key Control-q "quit"
```
保存并退出

这样在下次启动VMD时，就可以使用Control+q组合键退出了。

八. 安装MDAnalysis

使用conda安装

conda install -c conda-forge mdanalysis
# conda update mdanalysis # 升级
# conda install -c conda-forge MDAnalysisTests  # 安装测试数据

九. 安装MDTraj

使用conda安装
```
conda install conda-forge::mdtraj
```

十. 安装PyMol

使用conda安装

conda install -c conda-forge pymol-open-source

执行效果

su root
conda activate AmberTools23  # 切换到自己的conda环境
pymol xxxx.pdb

请添加图片描述

十一. 安装ChimeraX

执行以下命令

wget https://www.rbvi.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?ident=OHeQer2WSqdn9%2BJyqX5K%2BP9jvVBVQtzx0hx21QjmnvcirOjLdw%3D%3D&file=1.2%2Flinux%2FChimeraX-1.2.5.tar.gz&choice=Notified

下载下来 ChimeraX-1.2.5.tar.gz
解压
```
tar xvf ChimeraX-1.2.5.tar.gz
```

将解压目录拷贝到 /usr/local

cp chimerax-1.2.5-rc-2021.05.24/ /usr/local/ -r

在系统中创建软链接

ln -s /usr/local/chimerax-1.2.5-rc-2021.05.24/bin/ChimeraX /usr/bin/ChimeraX

安装效果，注意事项，ChimeraX 不要使用root用户和使用sudo权限运行
```
ChimeraX xxx.pdb
```
十二. 安装Namd

下载namd

wget https://www.ks.uiuc.edu/Research/namd/2.13/download/412487/NAMD_2.13_Linux-x86_64.tar.gz

解压
```
tar xvf NAMD_2.13_Linux-x86_64.tar.gz 
```

拷贝

cp NAMD_2.13_Linux-x86_64 /usr/local/ -r

创建软链接

ln -s /usr/local/NAMD_2.13_Linux-x86_64/namd2 /usr/local/bin/namd2

Centos7.9 部署分子动力学相关软件

Centos7.9 部署分子动力学相关软件

一. Centos7.9 基础工具安装及一些环境配置

1.1 Centos DNS配置

1.2 yum 换源

1.3 Centos7 yum只下载不安装, 离线安装

1.4 Centos7 安装 cmake3

1.5 其它基本工具安装

二. Centos7.9 使用scl+devtoolse-11 升级gcc

三. 安装fftw-3.3.8 (gromacs-2018.8的依赖)

四. 安装gromacs

4.1 gromacs-2018.8

4.2 gromacs-2022.6

五. 安装MiniConda 以及源的配置

六. 安装AmberTools23

七. 安装VMD

八. 安装MDAnalysis

九. 安装MDTraj

十. 安装PyMol

十一. 安装ChimeraX

十二. 安装Namd