基于xtb的amberQM/MM模拟

wuzhiyi

我知道可能很多人觉得用amber来跑QM/MM效率不是很高。但有些人就是懒，不想用别的，而且很多时候并不是想做非常严谨的QM，而是用一些半经验的方法试试看。
除掉那些历史悠久的半经验方法的话，amber自带的半经验能用的只有PM6和dftb3。amber的PM6只有DFT-D矫正，氢键矫正的形式有点怪。amber的dftb3又是连DFT-D矫正都没有。
所以我就想可以用现在大热的xtb来描述QM部分，无奈amber的QM/MM部分八百年没更新了，虽然有Holger Kruse写了一个amber/xtb的interface，但我记得是争对amber14的，现在再用可能会被审稿人欺负。
但从orca4.2开始，orca就支持xtb了，而amber支持orca，所以就可以串起来，搞一个amber/orca/xtb来用xtb。
可惜如果用orca/xtb的interface来调用xtb的话，point charge gradient文件pcgrad是以xtb的形式而非orca的形式输出，具体来说就是少了第一行point charge的个数和具体的小数点的个数也有点区别。
导致用orca/xtb生成的pcgrad文件无法被amber的amber/orca/的interface读取。
这个问题9月13号就被人提出在orca论坛上（https://orcaforum.kofo.mpg.de/viewtopic.php?f=11&t=5181&p=22867&hilit=xtb#p22867），不过没人理。于是我就修改的xtb一下（https://github.com/xiki-tempula/xtb），使其生成的pcgrad可以被amber的amber/orca来读取。发现我提供修改过的xtb之后，christoph.riplinger光速表示，我们会在下个版本修正这个问题，所以let‘s see。

具体操作就是把我修改过的xtb（https://github.com/xiki-tempula/xtb）下载下来，然后编译用intel编译器，meson（>0.49）和ninja编译。

1. export FC=ifort CC=icc CXX=icpc

复制代码

注意meson要新版的，直接git就行，meson不需要编译。

因为xtb强制静态编译，所以可能会遇到没有静态pthread库问题，我有一个修改版的xtb（https://github.com/xiki-tempula/xtb/tree/dendrite）用一种丑陋的方式解决了这个问题，不过据说xtb的人在改了。

然后把编译完成的xtb放到orca下面命名为otool_xtb
然后普通的用amber调用orca，提供名为orc_job.tpl的模版就行，注意修改内存和线程数。以及适当的定义qmcut，都用半经验了，就把整个蛋白都包进去吧，省的审稿人BB。
amber的输入文件 ua_equil.in (1.38 KB, 下载次数 Times of downloads: 47)

2019-11-11 04:34 上传 Uploaded

点击下载
Click to download
amber输入文件 和orc_job.tpl orc_job.tpl (41 Bytes, 下载次数 Times of downloads: 45)

2019-11-11 04:34 上传 Uploaded

点击下载
Click to download
orca模版 作为附件提供。

纪山

赞一个！

纪山

具体操作就是把我修改过的xtb（https://github.com/xiki-tempula/xtb）下载下来，---------------- 请问，下回来是 xtb-master.zip 文件吗？

wuzhiyi

纪山 发表于 2019-11-16 20:52
具体操作就是把我修改过的xtb（https://github.com/xiki-tempula/xtb）下载下来，---------------- 请问， ...

应该是
我一般就git clone https://github.com/xiki-tempula/xtb.git

纪山

wuzhiyi 发表于 2019-11-16 22:14
应该是
我一般就git clone https://github.com/xiki-tempula/xtb.git

用git clone的话又要安装一堆软件，好麻烦的说。

zsu007

谢谢分享！

ChaosChiao

厉害，能否写一个相关教程，付费也可。

wuzhiyi

ChaosChiao 发表于 2019-12-25 14:03
厉害，能否写一个相关教程，付费也可。

我觉得该有的信息都有了啊 你还要什么的教程啊？

霜晨月

编译时出了以下错误，请教楼主

xtb编译命令是按照社长写的编译xtb的教程：http://sobereva.com/521

[root@localhost xtb-master]# export FC=ifort CC=icc CXX=icpc
[root@localhost xtb-master]# meson setup build_intel --optimization=2
The Meson build system
Version: 0.52.1
Source dir: /mnt/hgfs/xtb_for_orca/xtb-master
Build dir: /mnt/hgfs/xtb_for_orca/xtb-master/build_intel
Build type: native build
Project name: xtb
Project version: 6.2.1
Fortran compiler for the host machine: ifort (intel 12.1.0 "ifort (IFORT) 12.1.0 20110811")
Fortran linker for the host machine: xild 12.1.0
C compiler for the host machine: icc (intel 12.1.0 "icc (ICC) 12.1.0 20110811")
C linker for the host machine: xild 12.1.0
C++ compiler for the host machine: icpc (intel 12.1.0 "icpc (ICC) 12.1.0 20110811")
C++ linker for the host machine: xild 12.1.0
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program git found: YES (/usr/bin/git)
Program date found: YES (/usr/bin/date)
Program whoami found: YES (/usr/bin/whoami)
Program hostname found: YES (/usr/bin/hostname)
Configuring xtb_version.fh using configuration
WARNING: Consider using the builtin option for language standard version rather than adding flags by hand.
WARNING: Consider using the builtin option for language standard version rather than adding flags by hand.
Library pthread found: YES
Library m found: YES
Library dl found: YES
Library mkl_intel_lp64 found: YES
Library mkl_intel_thread found: YES
Library mkl_core found: YES
Library iomp5 found: YES
Library mkl_rt found: YES
Run-time dependency threads found: YES
Program a2x found: NO
Program pytest found: NO
Program mypy found: NO
Program pylint found: NO
Program flake8 found: NO
Build targets in project: 5
Found ninja-1.7.2 at /usr/bin/ninja-build


[root@localhost xtb-master]# ninja -C build_intel
bash: ninja: command not found...

因为前面ninja的安装没有报错，所以我尝试将ninja改为ninja-build：会不会是这步的问题？


[root@localhost xtb-master]# ninja-build -C build_intel
ninja: Entering directory `build_intel'
[1/279] Compiling Fortran object 'xtb@sta/xtb_tbdef_param.f90.o'.
FAILED: xtb@sta/xtb_tbdef_param.f90.o
ifort -Ixtb@sta -I. -I.. -I../include -warn general -warn truncated_source -O2 -g -axAVX2 -r8 -traceback -qopenmp -D_FILE_OFFSET_BITS=64 -fPIC -module xtb@sta '-gen-dep='xtb@sta/xtb_tbdef_param.f90.o'' -gen-depformat=make -o 'xtb@sta/xtb_tbdef_param.f90.o' -c ../xtb/tbdef_param.f90
ifort: command line warning #10130: unknown extension 'A' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'V' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'X' ignored in option '-ax'
ifort: command line warning #10130: unknown extension '2' ignored in option '-ax'
ifort: command line warning #10006: ignoring unknown option '-qopenmp'
../xtb/tbdef_param.f90(79): error #8040: Invalid type-name in a derived type definition.   [GFN_PARAMETER]
   type gfn_parameter(nelem,nshell)
--------^
../xtb/tbdef_param.f90(80): error #6659: Not an attribute-spec keyword   [LEN]
      integer, len :: nelem  = max_elem
---------------^
../xtb/tbdef_param.f90(81): error #6659: Not an attribute-spec keyword   [LEN]
      integer, len :: nshell = max_shell
---------------^
../xtb/tbdef_param.f90(83): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [EN]
      real(wp) :: en(nelem)
------------------^
../xtb/tbdef_param.f90(84): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [MC]
      real(wp) :: mc(nelem)
------------------^
../xtb/tbdef_param.f90(85): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [GAM]
      real(wp) :: gam(nelem)
------------------^
../xtb/tbdef_param.f90(86): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [GAM3]
      real(wp) :: gam3(nelem)
------------------^
../xtb/tbdef_param.f90(87): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [RAD]
      real(wp) :: rad(nelem)
------------------^
../xtb/tbdef_param.f90(88): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [WLL]
      real(wp) :: wll(nelem,nshell)
------------------^
../xtb/tbdef_param.f90(89): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [REP]
      real(wp) :: rep(2,nelem)
------------------^
../xtb/tbdef_param.f90(90): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [POLYR]
      real(wp) :: polyr(4,nelem)
------------------^
../xtb/tbdef_param.f90(91): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [CXB]
      real(wp) :: cxb(nelem)
------------------^
../xtb/tbdef_param.f90(92): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [AO_EXP]
      real(wp) :: ao_exp(nshell,nelem)
------------------^
../xtb/tbdef_param.f90(93): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [AO_LEV]
      real(wp) :: ao_lev(nshell,nelem)
------------------^
../xtb/tbdef_param.f90(94): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [LPAR]
      real(wp) :: lpar(0:2,nelem)
------------------^
../xtb/tbdef_param.f90(95): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [KPAIR]
      real(wp) :: kpair(nelem,nelem)
------------------^
../xtb/tbdef_param.f90(96): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [KCNAT]
      real(wp) :: kcnat(0:2,nelem)
------------------^
../xtb/tbdef_param.f90(97): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [RADAES]
      real(wp) :: radaes(nelem)
------------------^
../xtb/tbdef_param.f90(98): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [DPOLC]
      real(wp) :: dpolc(nelem)
------------------^
../xtb/tbdef_param.f90(99): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [QPOLC]
      real(wp) :: qpolc(nelem)
------------------^
../xtb/tbdef_param.f90(100): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [AO_PQN]
      integer  :: ao_pqn(nshell,nelem)
------------------^
../xtb/tbdef_param.f90(101): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [AO_L]
      integer  :: ao_l(nshell,nelem)
------------------^
../xtb/tbdef_param.f90(102): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [AO_N]
      integer  :: ao_n(nelem)
------------------^
../xtb/tbdef_param.f90(103): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [AO_TYP]
      integer  :: ao_typ(nshell,nelem)
------------------^
../xtb/tbdef_param.f90(104): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [METAL]
      integer  :: metal(nelem)
------------------^
../xtb/tbdef_param.f90(105): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [CNVAL]
      integer  :: cnval(nelem)
------------------^
../xtb/tbdef_param.f90(106): error #6530: The array spec for this component must be of explicit shape and each bound must be an initialization expression.   [TIMESTP]
      character(len=30) :: timestp(nelem)
---------------------------^
../xtb/tbdef_param.f90(83): error #6279: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association   [NELEM]
      real(wp) :: en(nelem)
---------------------^
../xtb/tbdef_param.f90(88): error #6279: A specification expression object must be a dummy argument, a COMMON block object, or an object accessible through host or use association   [NSHELL]
      real(wp) :: wll(nelem,nshell)
----------------------------^
compilation aborted for ../xtb/tbdef_param.f90 (code 1)
[2/279] Compiling Fortran object 'xtb@sta/xtb_tbdef_setvar.f90.o'.
ifort: command line warning #10130: unknown extension 'A' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'V' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'X' ignored in option '-ax'
ifort: command line warning #10130: unknown extension '2' ignored in option '-ax'
ifort: command line warning #10006: ignoring unknown option '-qopenmp'
[3/279] Compiling Fortran object 'xtb@sta/xtb_tbdef_data.f90.o'.
ifort: command line warning #10130: unknown extension 'A' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'V' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'X' ignored in option '-ax'
ifort: command line warning #10130: unknown extension '2' ignored in option '-ax'
ifort: command line warning #10006: ignoring unknown option '-qopenmp'
[4/279] Compiling Fortran object 'xtb@sta/xtb_tbdef_wavefunction.f90.o'.
ifort: command line warning #10130: unknown extension 'A' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'V' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'X' ignored in option '-ax'
ifort: command line warning #10130: unknown extension '2' ignored in option '-ax'
ifort: command line warning #10006: ignoring unknown option '-qopenmp'
[5/279] Compiling Fortran object 'xtb@sta/xtb_tbdef_basisset.f90.o'.
ifort: command line warning #10130: unknown extension 'A' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'V' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'X' ignored in option '-ax'
ifort: command line warning #10130: unknown extension '2' ignored in option '-ax'
ifort: command line warning #10006: ignoring unknown option '-qopenmp'
[6/279] Compiling Fortran object 'xtb@sta/xtb_tbdef_solvent.f90.o'.
ifort: command line warning #10130: unknown extension 'A' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'V' ignored in option '-ax'
ifort: command line warning #10130: unknown extension 'X' ignored in option '-ax'
ifort: command line warning #10130: unknown extension '2' ignored in option '-ax'
ifort: command line warning #10006: ignoring unknown option '-qopenmp'
ninja: build stopped: subcommand failed.


另外请教一下，网站直接打包下载的xtb-master.zip解压之后6.9MB，git clone下来的目录为8.5MB，而Grimme提供的编译好的xtb有30多MB，是不是不对？是不是两种方式下载的source code都不完整？（按理说编译成二进制可执行文件之后体积会大大缩小）

wuzhiyi

霜晨月 发表于 2019-12-26 16:06
编译时出了以下错误，请教楼主

xtb编译命令是按照社长写的编译xtb的教程：http://sobereva.com/521

你把ninja加进path没有啊
xtb静态编译 体积变大不奇怪

霜晨月

wuzhiyi 发表于 2019-12-28 02:30
你把ninja加进path没有啊
xtb静态编译 体积变大不奇怪

正确设置了ninja的soft link，这次可以直接找到ninja了，但第三步的报错跟原来一样
怀疑可能是我的ifort的问题
申请了个2019的intel编译包，四五天了还没消息。。

wuzhiyi

霜晨月 发表于 2019-12-28 22:32
正确设置了ninja的soft link，这次可以直接找到ninja了，但第三步的报错跟原来一样
怀疑可能是我的ifort ...

ifort居然会有问题，我建议你去github上提个issue

霜晨月

折腾了N天，终于编译出来了，简单报告一下结果。

ifort和icc尝试了好几个版本，最后用的是Intel compilers_and_libraries_2019.1.144（就是2019 update 1）。
编译出来的xtb 18MB，比官方的版本小了不少，不知道怎么回事。
这个xtb运行时还要依赖Intel compilers_and_libraries_2019.1.144，看来这个6.7GB的toolkit只能一直留着了。

测速结果：
硬件Xeon E5-2699 v4 双路，主频 2.20GHz
Amber18，gfortran编译（之前我也用ifort编译过，但速度与gfortran版本无明显差别，且MM/PBSA工具无法使用，后来被我删了）
orca版本是 4.2.1
sander都用串行版单核运行。步长 1 fs。
QM region 102 atoms: 43 ps/day
QM region 144 atoms: 25.6 ps/day
感觉并行效率很差，单核和2核（%pal nprocs 2 end）速度看不出差别。其实，即便是单核运行时，sander和otool_xtb的CPU占用也达不到100%，连70%都很难达到。估计是三个程序来回调用，大部分时间花费在中间的折腾上了。

粗测结果仅供参考哈，如果我的设置有什么问题敬请达人指正^_^

wuzhiyi

霜晨月 发表于 2020-1-6 14:26
折腾了N天，终于编译出来了，简单报告一下结果。

ifort和icc尝试了好几个版本，最后用的是Intel compile ...

我也觉得效率差，主要时间都在读写文件上了，不过我感兴趣的东西一般20ps就好收敛，挂一晚上第二天就好。。。所有也没动力。

纪山

wuzhiyi 发表于 2019-11-16 22:14
应该是
我一般就git clone https://github.com/xiki-tempula/xtb.git

，虽然有Holger Kruse写了一个amber/xtb的interface，   ------------------  请问，Holger Kruse 的这篇关于amber/xtb的interface 文献 名字叫什么呀？