Molclus:简便实用的团簇构型和分子构象搜索程序



最新版本:1.9.9.9 (2022-Mar-6发布,2022-Jun-24最后更新)

Index of this page:
下载 引用方式 简介 使用说明 使用咨询 更新历史 使用Molclus已发表的学术文章

下载:

最新版Molclus程序包的可执行文件可在此免费下载:Windows版Linux 64bit版。没有Mac版。源代码不公开提供。

引用方式:

如果Molclus(无论是其中哪个组件)在你的文章中被使用,都必须在正文进行引用引用格式为
Tian Lu, Molclus program, Version x.x, http://www.keinsci.com/research/molclus.html (accessed 月 日, 年)
x.x代表实际版本号。具体格式可根据期刊要求修改。如果没有按要求引用,一经发现将被列入黑名单,禁止在未来使用Molclus,并且会在本页面里进行公示。另:我们未来会专门发表论文对Molclus进行介绍,届时会在本页面提供文章信息,之后请引用论文而不要再引用网址,目前发表文章必须按照上述说明引用。

如果在Molclus中调用了Shermo程序计算了热力学量,也务必同时按照Shermo程序主页(http://sobereva.com/soft/shermo)上的说明恰当引用Shermo程序原文

简介:

Molclus是一款团簇构型搜索和分子构象搜索的程序,由卢天(北京科音自然科学研究中心)开发。优点有:

由于上述优点,稍微熟悉Molclus后会觉得比用很多动辄几千甚至上万元的昂贵的商业程序做构型、构象搜索好用得多,不仅精度高得多得多,也明显更灵活和方便。而那些收费昂贵且只支持分子力场进行构象搜索的商业程序其实根本没什么实际用处,又不灵活,精度又实在太差。

Molclus已经被大量研究者们使用并在JACS Au、Adv. Funct. Mater.、Sci. Adv.、Carbon、Chem. Eur. J.、J. Mater. Chem.等高水平的刊物上发表了优秀的文章,使用Molclus已发表的文章列表请点击此处查看。

下图是利用Molclus对(H2O)4团簇和麻黄碱进行构型/构象搜索的结果的例子,由免费的VMD程序载入molclus的结果文件绘制

    

下图是Molclus搜索出的Li6团簇的三种构型

下图是Molclus搜索出的治疗2019年12月开始蔓延的COVID-19肺炎的特效药瑞德西韦(Remdesivir)在水环境下常温时自由能最低的两种构象和Boltzmann分布比例,图像由ChimeraX绘制

 

使用说明:

极其详细、易懂的Molclus的使用介绍与实例(这个就是现阶段的手册)

有molclus用户针对在集群上通过PBS作业提交方式使用molclus的方法做了介绍,见:http://bbs.keinsci.com/thread-15598-1-1.html

基本使用流程

记录初始结构的traj.xyz文件既可以通过molclus自带的产生初始团簇构型的genmer工具或产生分子初始构象的gentor工具生成,也可以通过GROMACS、xtb等程序跑分子动力学或者做模拟退火产生,也可以用专门的构象生成程序如Confab产生。然后molclus会对traj.xyz记录的所有或部分结构自动调用收费的Gaussian或免费的ORCA、MOPAC、xtb、Open Babel进行优化或单点或振动分析计算,并对结果通过自带的isostat工具进行去重和按照能量排序。

使用基本流程图如下。青色方框是molclus自身的组件,椭圆包围的文件名是运行过程中涉及的文件

Molclus通常有以下使用方式:

Molclus可以调用的用于计算能量、优化的程序有以下程序。完全覆盖小体系高精度计算和巨型体系粗放计算

使用咨询:

在计算化学公社论坛(http://bbs.keinsci.com)的量子化学版发帖咨询,发帖时请选择"Molclus"分类。如果发现程序里有bug也非常欢迎发帖报告。


更新历史

2022-Mar-6:1.9.9.9版发布
2022-Jun-24:最后更新

• Molclus判断traj.xyz中要忽略的结构时支持了对原子间距离更精细的控制。在settings.ini里若将distmax设为0,molclus启动后就会从当前目录下的distrange.txt里读取设置,其中每一行的格式为:原子组1序号 原子组2序号 最近距离 最远距离,距离单位为埃。例如,若此文件内容为1,3-5 2,8 2.5 10.2,就代表1,3,4,5和2,8这两批原子间最小距离必须大于2.5埃,最大距离不能超过10.2埃,如果traj.xyz里某结构违背了这个条件,则这个结构就会被跳过而不计算。distrange.txt里可以设多行,同时满足所有条件的结构才被计算。
• 2022-May-28修正了一个bug:isostat用-Edis设置判断重复结构的能量阈值时单位转换有问题
• 2022-Jun-8修正了genmer的$distcons设置存在的bug
• 2022-Jun-14使molclus完全兼容了Windows版xtb
• 2022-Jun-24修正了molclus调用xtb时settings.ini里freeze设置不生效的bug

2022-Mar-3:1.9.9.8版发布
• genmer组件的genmer.ini里的ishuffle选项现在可以设负值。如果设-N,则前N类分子插入的时候还是按顺序插入,而其余的分子则随机顺序插入。这对于构建很多体系很有用,比如构建某个溶质分子被两类分子混合构成的溶剂层包围,可以在genmer.ini里把溶质设为第一类分子,而第2、3类分子设成两种溶剂分子,并把ishuffle设为-1,这样构造出的体系中溶质分子肯定出现在中心。

2021-Nov-23:1.9.9.7版发布
• Molclus的settings.ini里现可以把energyterm参数设为"TD=",此时如果Gaussian模板文件对应的是TDDFT计算,Molclus会从Gaussian输出文件里读取TDDFT算的root指定的态的激发态能量。由此可以实现用molclus做激发态构象搜索或者激基复合物构型搜索。

2021-Sep-4:1.9.9.6版发布
2021-Sep-29:最后更新
• molclus的setting.ini设置文件里现在可以设置热力学量计算程序Shermo(http://sobereva.com/soft/shermo/)的路径和运行参数,当molclus调用Gaussian或ORCA做freq或opt freq任务后会自动调用Shermo来算热力学量,比Gaussian和ORCA自身算热力学数据的代码更灵活、强大、可靠。见《使用molclus程序做团簇构型搜索和分子构象搜索》(http://bbs.keinsci.com/thread-577-1-1.html)里加入的说明。
• genmer组件的genmer.ini设置文件里现在可以在末尾加入一行$distcons,然后下面通过一行或多行,指定一对或多对元素间必须满足的距离范围(没设的话就不做限制),指定特定元素间必须满足的距离范围(没设的话就不做限制),例如写H Mg 2.0就代表氢和镁之间距离不能小于2.0埃,Pt Pt 1.8 3.2代表铂之间距离必须在1.8~3.2埃。违背约束条件的构型会被视为失败而不输出。genmer.ini末尾还可以加入一行$modrad,然后在下面通过一行或多行,对一个或多个元素半径进行修改,比如Pt 3.5就把半径改为了3.5埃。详见《genmer:生成团簇初始构型的超便捷工具》(http://bbs.keinsci.com/thread-2369-1-1.html)里面新加入的说明和例子。
• genmer组件启动时如果发现当前目录下没有genmer.ini,将会提示用户手动输入配置文件路径,因此不是非得叫genmer.ini且放在当前目录不可了。molclus启动时如果发现当前目录下没有traj.xyz和settings.ini,也会直接让用户手动输入它们的路径。
• 修正了一个bug:molclus组件调用OpenBabel时产生的临时xyz文件里元素名都是大写,导致双字符的原子如Cl在OpenBabel用力场计算的时候没法正常指认原子类型。

2021-Jul-4:1.9.9.5版发布
2021-Aug-28:最后更新

• genmer组件的genmer.ini设置文件里现在可以用xmin、xmax、ymin、ymax用于控制分子出现的X、Y范围,和之前版本里的zmin、zmax用处类似。因此目前可以严格控制指定的分子出现的三维空间范围。
• xyz2QC组件的Gaussian模板文件中现在可以使用[FILENAME]占位,产生输入文件时它将被替换为"前缀 帧号",因此可以在模板文件里写比如%chk=/sob/[FILENAME].chk从而使得计算完毕后chk文件以恰当的名字留存在/sob目录下。

2021-Apr-15:1.9.9.4版发布
• isostat组件可以通过命令行运行并结合各种参数,更为强大也更便于嵌入到脚本里。比如执行isostat Rize.xyz -Nout 8 -Eout 2.4 -Edis 0.5 -Gdis 0.2 -T 350 -nt 32命令,代表将Rize.xyz 作为输入文件,往cluster.xyz里导出的簇是能量最低的8个且相对能量还必须在2.4 kcal/mol以内。使用0.5 kcal/mol和0.2埃分别作为归簇的能量和几何偏差判据。计算Boltzmann分布使用350K。使用32个线程并行计算。凡是通过命令行指定的参数就不需要在交互式界面里再输入。

2021-Feb-11:1.9.9.3版发布
• genmer的genmer.ini文件中现在允许写noxrot、noyrot、nozrot分别要求单体不能绕X、Y、Z轴随机旋转。也可以同时写两个,比如noxrot noyrot要求单体只能绕Z轴随机旋转。

2020-Dec-28:1.9.9.2版发布
• 解决了某些情况下Gaussian几何优化没收敛时Molclus会卡住的问题。

2020-Dec-10:1.9.9.1版发布
• 当molclus的settings.ini的igaucontinue=1时,如果Gaussian做优化失败后基于template2.gjf继续优化还没成功,这个新版本程序会试图基于当前目录下的template3.gjf继续进行优化,因此用户对于难收敛的情况可以有更多备选方案。

• settings.ini里对ORCA用户新增了ibkhess选项。若=1且任务涉及到振动分析,ORCA产生的.hess文件会被自动备份为 orca[序号].hess文件,便于用户之后重新利用Hessian。

2020-Oct-28:1.9.9版发布
2020-Nov-16:最后更新
• 加入了mol2_xyz组件,主要用于将Frog2构象生成程序产生的多帧mol2文件转换成traj.xyz文件,这种做法的意义见molclus新的教程《将Confab或Frog2与Molclus联用对有机体系做构象搜索》。
• 新特性:当当前目录下出现名为STOP的文件时,molclus对traj.xyz里各个结构的循环将被强行终止(每开始算一个新的结构时探测一次)。因此在当前目录下创建名为STOP的文件是一种优雅的强制结束molclus运行的做法。
• 新特性:如果isomers.xyz是molclus做优化+振动分析或振动分析任务产生的,isostat在处理时会报告哪些构型存在虚频。
• 改进:支持了目前最新版的crest程序输出的crest_ensemble.xyz

2020-Oct-17:1.9.8版发布
2020-Oct-18:最后更新
• 显著加快了isostat排序时候的速度,对于帧数非常多的情况甚至比老版本快一个数量级。
• 当molclus的settings.ini中iappend=1(续写模式)时,程序启动时不会自动将当前目录下.out、.chk、orca开头的文件删掉(因为这些可能是之前用ibkout、ibkchk等选项保留下来的有意义的文件)。
• 让ibkout、ibkchk等选项保留出来的文件的文件名中的序号与traj.xyz里帧号保持了一致(以前版本总是从1开始计)。这使得利用iappend=1时可以跑多次molclus将traj.xyz里的所有帧分别算完,确保每次备份出来的文件序号不会彼此覆盖

2020-Oct-14:1.9.7版发布
• molclus的settings.ini里新增加了iappend选项。如果设为1,新产生的结构会累加到当前目录下之前的isomers.xyz文件(如果有的话)末尾。如果为0,则原先的isomers.xyz会被新的数据覆盖。
• gentor的gentor.ini中若在旋转设置后面空一行写上reportfail=1,则会将未通过检查的构象的失败原因显示出来,判断是由于哪些原子间距离太近导致未通过检测。默认的critskip参数的阈值从0.8减小为了0.75,避免含有氰基的时候容易出现难以通过检测的情况。
• 如果运行gentor时当前目录下没发现mol.xyz或gentor.ini,会提示用户直接输入这两种文件的路径(文件名随意)

2020-Jul-12:1.9.6版发布
• 解决了itask=3且没有基于单点模板文件自动做高精度单点计算的时候,在isomers.xyz里记录的能量为0的bug(本应记录的是freq任务给出的自由能)。

2020-Jun-1:1.9.5版发布
• 将isostat组件做了并行化。当要处理的帧数很多的时候(好几千),在核数较多的机子上耗时可以降低一个数量级。

2020-Apr-21:1.9.4版发布
• 修正了itask=3且没有提供单点任务模板文件时给出的能量有误的bug。

2020-Feb-11:1.9.3版发布
• 兼容了crest程序的-mdopt任务产生的crest_ensemble.xyz文件(即可以当做isomers.xyz文件来被isostat处理。只要发现文件名里有crest字样就按照这种格式来读取)。

2020-Feb-5:1.9.2版发布
• 已支持在振动分析(itask=2)或优化+振动分析(itask=3)之后自动用高精度级别算单点能,从而直接给出较好精度的自由能。具体做法是在当前目录下提供template_SP.gjf(template_SP.inp)文件,设置Gaussian(ORCA)高精度单点计算的关键词,格式同template.gjf(template_SP.inp)。之后,当优化或优化+振动分析任务结束后,程序发现当前目录下有template_SP.gjf(template_SP.inp)时就会用其中的信息构成单点任务文件并调用Gaussian(ORCA)计算,并自动将新的单点能与自由能热校正量相加作为最终能量输出。几个细节:
(a)如果template_SP.gjf和template_SP.inp同时存在,优先考虑template_SP.inp
(b)opt、opt freq任务用的程序与自动算高精度单点的可以不同,比如iprog=1调用Gaussian时也可以通过提供template_SP.inp来令程序自动调用ORCA算高精度单点
(c)利用template_SP.gjf基于Gaussian自动算高精度单点时,Gaussian用户还需在settings.ini里对energyterm参数恰当设置,用于指定如何读取这个级别的单点任务输出文件里的能量
• 为提升灵活性,molclus支持了直接指定设置文件和初始结构文件的路径。例如molclus /RAS/Layer.ini代表将/RAS/Layer.ini作为设置文件。再比如molclus lock.ini /RAS/chu2.xyz代表用当前目录下的lock.ini的设定对/RAS/chu2.xyz里的结构进行计算。

2020-Jan-19:1.9.1版发布
• 兼容了2019年12月18日发布的xtb 6.3版预览版,对老版本xtb不再兼容。

2019-Nov-5:1.9版发布
• molclus的settings.ini支持了itask=2(振动分析)和itask=3(几何优化+振动分析),可结合Gaussian、ORCA和xtb使用。做这些任务时molclus会提取自由能、自由能热校正量、虚频数目,在屏幕上输出的同时也写入到isomers.xyz。之前版本里针对xtb的itask=-2被撤掉(已被itask=3代替)
• 去掉了molclus的settings.ini中意义不大的xtb_path(因为xtb运行命令是固定的)
• 在执行计算任务之前会对模板文件内容进行检查

2019-Sep-28:1.8.9版发布
• 更新了isostat。改进在于将某isomer纳入已有的簇的时候,如果这个isomer的能量比那个簇的能量更低,则这个簇的结构和能量将会被这个isomer的所代替。另外,从本版本开始的Windows版中,isostat.exe对应64bit版,而isostat_32bit.exe对应32bit版。
• 当ibkout>0而MOPAC运行没有正常结束(没生成arc)的时候,原先版本无法备份文件,而当前版本会将out进行备份。
• gentor里的critskip参数的默认值从原来的0.5改大为了0.8,避免得到的初始结构里有一些原子因为离得太近在优化后变成诡异结构。
• 修正了itask=0的时候与最新版xtb不兼容的问题

2019-Aug-12:1.8.8版发布。完美支持了近期发布的ORCA 4.2(之前版本的备份优化轨迹文件的功能不兼容ORCA 4.2)。从此molclus不再完美支持ORCA 4.2以前的版本

2019-Aug-7:1.8.7版发布。调用xtb之前会自动删除xtbrestart文件,减小了对某些体系调用最新版xtb程序优化失败的几率。

2019-Jul-28:1.8.6版发布。molclus支持了冻结原子,通过settings.ini里的freeze设置,如设成2,5-8,12-14代表在涉及优化的任务中将2,5,6,7,8,12,13,14号原子的XYZ笛卡尔坐标冻结。此选项对调用Gaussian、xtb、ORCA、MOPAC的情况皆生效。借助此选项可以实现诸如过渡态结构的构象搜索(即反应的区域冻结而只对其余部分进行构象搜索)。

2019-Jul-1:1.8.5版发布。molclus支持了对traj.xyz里完全自定义帧号范围进行计算,通过settings.ini里的ngeom设置,如设成2,5-8,12-14代表只处理第2,5,6,7,8,12,13,14帧

2019-Jun-12:1.8.4版发布。gentor程序的gentor.ini里增加了critskip选项,如果gentor产生的结构中有任意两个原子间距离小于两个原子共价半径乘以critskip值的话,则这个构象将不被输出到traj.xyz中(critskip默认值为0.5,这也是之前版本用的数值)。此外,molclus里ieneonly选项的名字改为了itask,其中增加了选项-2,此时若调用xtb将会做优化和振动分析(即--ohess任务),并且molclus读取的是自由能而非电子能量。

2019-May-26:1.8.3版发布。genmer程序的genmer.ini里增加了ngenmust选项,用于要求genmer运行结束前必须成功生成多少个构型,而不是像ngen选项那样指定的是期望生成多少个构型(其中有的可能生成失败)。

2019-May-15:1.8.2版发布(最后更新于2019-May-21)。改进了xyz2QC组件,产生单独的Gaussian或ORCA输入文件时现已可以指定文件名前缀,而且产生单独的Gaussian输入文件时会自动保留chk文件。给molclus的settings.ini增加了ibkgbw选项,可以让molclus调用ORCA计算每个体系后将gbw自动备份。

2019-Mar-30:1.8.1版发布。molclus的settings.ini里的ieneonly选项增加了-1,表示任务是调用Gaussian做热力学组合方法的计算。此时如果将template.gjf里的关键词设为比如G4,将energyterm=设为"G4 Free Energy=",则molclus提取的将是G4热力学组合方法算的高精度自由能。同时,此版本对settings.ini的格式做了轻微修改,并去掉了没用的isys选项。
此版本也更新了isostat,当归簇后簇的数目非常大(>500)时,会提示是否只保留用户指定数目的能量最低的簇,由此可避免屏幕上输出的簇的信息量过大、产生的cluster.xyz文件过大。同时给《gentor:扫描方式做分子构象搜索的便捷工具》文章增加了第4节,给出了通过molclus结合xtb和ORCA程序实现高度柔性分子精确构象搜索的实例。

2019-Mar-20:1.8版发布。扩展了genmer的功能,增加了rmin、zmax和zmin选项,从而能轻松地构造笼状团簇、平面团簇、环状团簇、桶状团簇的初猜结构,并进而结合molclus优化这些团簇的实际结构,这对于原子团簇研究很重要。请查看已更新的genmer的帖子了解详情。

2019-Mar-17:1.7版发布。新添加了xyz2QC工具,用于将molclus/genmer/gentor产生的多帧.xyz文件转化成Gaussian或ORCA的输入文件(含多步任务的单一文件或者一批单独的文件),便于用户往超算上直接提交。点此链接查看详情。

2019-Feb-12:1.6版发布。大幅扩展了genmer和gentor的功能,并令molclus兼容2019-Feb-8发布的xtb。点此链接查看详情。

2019-Jan-1:为造福广大计算化学工作者,molclus从此由收费变为免费!

2018-Aug-28:1.5版发布。支持了Open Babel(http://openbabel.org),这是免费的格式转换程序,同时附带基于力场的计算功能。通过令molclus调用此程序可以实现基于MMFF94、GAFF、UFF等力场的几何优化和能量计算任务。

2018-Jun-25:1.4.3版发布。对xtb程序作了更好的支持,可以指定运行选项。另外对gentor进行了升级,现在可以用比如e5 120 140来让片段依次旋转120,125,130,135,140度。同时修正了一些bug。

2017-Dec-1:1.4版发布。支持了Grimme开发的做GFN-xtb (见J. Chem. Theory Comput., 13, 1989)计算的xtb程序(可由此免费获得https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/xtb/xtb)。settings.ini里增加了mpioption选项,用于设定Linux下ORCA并行运行时给mpirun的额外参数,例如root用户下运行需要的--allow-run-as-root。

2016-Sep-16:1.3.5版发布。修正了一个某些情况下无法正确读取优化的结构,有时还会导致死循环的bug。

2016-Aug-16:1.3.4版发布。gentor可以现在可以直接设定原子间是否成键,以及设定成键阈值。

2016-Jul-10:1.3.3版发布。修正了gentor无法剔除含有原子过近接触的结构的bug。修正了对计算时间统计的bug。

2016-Jun-18:1.3.2版发布。通过settings.ini里的ibkchk可以将Gaussian对每个结构计算产生的.chk文件进行保留。

2016-Apr-28:1.3.1版发布。此版本修正了读取ORCA优化任务能量错误问题。并且可以靠ngeom参数选择只考虑traj.xyz中某一范围的结构。

2015-Dec-18:1.3版发布。此版本加入了gentor子程序用于通过扫描方式产生分子构象搜索用的初始结构。

2015-Dec-15:1.2版发布。此版本加入了genmer子程序用于方便地批量产生团簇构型的初始结构。isostat增加了输出波尔兹曼分布的功能。

2015-Feb-8:1.1版发布。此版本对所含isostat进行了升级,在对结构归簇时,不仅对比能量,还对比几何结构偏差,都小于设定的阈值时才被归到一个簇里。由此可以区分开能量接近简并的不同构型/构象。

2015-Jan-5:1.0版发布


用户们使用Molclus已发表的文章

由新到旧排序

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