https://github.com/agiliopadua/fftool
http://m3g.iqm.unicamp.br/packmol/home.shtml
2020年8月8日 星期六
2020年7月22日 星期三
2020年6月13日 星期六
2020年6月9日 星期二
2020年4月16日 星期四
用Gaussian算partial charge
Job Type:
1.選Opt+Freq
2.Additional Keywords: pop=chelpg
Method:
1.選DFT
跑完用關鍵字esp找最後一步的ESP charges
2020年3月30日 星期一
psf格式
PSF specification
CHARMM
Normal (standard) and extended (EXT) PSF format are supported. CHEQ is supported in the sense that CHEQ data is simply ignored.
CHARMM Format from
source/psffres.src:
CHEQ:
II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I),ECH(I),EHA(I)
standard format:
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8,2G14.6)
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,A4,1X,2G14.6,I8,2G14.6) XPLOR
expanded format EXT:
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8,2G14.6)
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8,2G14.6) XPLOR
no CHEQ:
II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I)
standard format:
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8)
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,A4,1X,2G14.6,I8) XPLOR
expanded format EXT:
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8)
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8) XPLOR
參考
https://www.mdanalysis.org/UserGuide/formats/reference/psf.html
http://www.charmm-gui.org/?doc=lecture&module=pdb&lesson=6
2020年3月28日 星期六
ubuntu 18.04 install Packmol
1.下載檔案
http://m3g.iqm.unicamp.br/packmol/download.shtml
2.解壓縮
$ tar -xvzf packmol.tar.gz
3.make
$ make
4.設定packmol環境
$ sudo cp packmol /usr/local/bin
5.編譯packmol
$ packmol < mixture.inp
http://m3g.iqm.unicamp.br/packmol/download.shtml
2.解壓縮
$ tar -xvzf packmol.tar.gz
3.make
$ make
4.設定packmol環境
$ sudo cp packmol /usr/local/bin
5.編譯packmol
$ packmol < mixture.inp
Mac install Packmol
1.先安裝gfortran
$ brew cask install gfortran
2.下載檔案
http://m3g.iqm.unicamp.br/packmol/download.shtml
3.解壓縮
$ tar -xvzf packmol.tar.gz
4.讓腳本可執行
$ chmod +x ./configure
5.執行腳本
$ ./configure
6.設定packmol環境
$ sudo cp packmol /usr/local/bin
7.編譯packmol
$ packmol < mixture.inp
$ brew cask install gfortran
2.下載檔案
http://m3g.iqm.unicamp.br/packmol/download.shtml
3.解壓縮
$ tar -xvzf packmol.tar.gz
4.讓腳本可執行
$ chmod +x ./configure
5.執行腳本
$ ./configure
6.設定packmol環境
$ sudo cp packmol /usr/local/bin
7.編譯packmol
$ packmol < mixture.inp
2020年3月16日 星期一
使用Press/berendsen常常發生Cuda driver error 700 in call at file 'geryon/nvd_timer.h' in line 76.
使用berendsen注意事項
fix 1 all nve
fix 2 all langevin 300.0 300.0 1000.0 699483
1.要搭配nve才能透過積分找出下一步v跟f
2.先使用langevin 讓系統達到平衡再呼叫temp/berendsen和press/berendsen，以下是axel的解釋
the thermo output suggests that your system is far from equilibrium,
i would first run for a while with fix nve and fix langevin (using an
adequately high friction term) that will help to bring your system
closer to equilibrium and also help dissipating the kinetic energy
evenly throughout your system. once this has stabilized, and only
then, you should switch to a variable volume fix. this has been
discussed here several times already.
參考
https://sourceforge.net/p/lammps/mailman/message/25173729/
fix 3 all temp/berendsen 300.0 300.0 500
fix 4 all press/berendsen iso 1.0 1.0 1000
3.Pdamp要設至少1000才能夠跑
參考
https://lammps.sandia.gov/doc/fix_press_berendsen.html
fix 1 all nve
fix 2 all langevin 300.0 300.0 1000.0 699483
1.要搭配nve才能透過積分找出下一步v跟f
2.先使用langevin 讓系統達到平衡再呼叫temp/berendsen和press/berendsen，以下是axel的解釋
the thermo output suggests that your system is far from equilibrium,
i would first run for a while with fix nve and fix langevin (using an
adequately high friction term) that will help to bring your system
closer to equilibrium and also help dissipating the kinetic energy
evenly throughout your system. once this has stabilized, and only
then, you should switch to a variable volume fix. this has been
discussed here several times already.
參考
https://sourceforge.net/p/lammps/mailman/message/25173729/
fix 3 all temp/berendsen 300.0 300.0 500
fix 4 all press/berendsen iso 1.0 1.0 1000
3.Pdamp要設至少1000才能夠跑
參考
https://lammps.sandia.gov/doc/fix_press_berendsen.html
2020年3月11日 星期三
oplsaa轉到LAMMPS
tinker
https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
oplsaa-erg_ff
https://bitbucket.org/comcon1/oplsaa-erg_ff/src/default/
Dihedral Coeffs
https://lammps.sandia.gov/threads/msg32415.html
Moltemplate OPLS-AA improper parameters
https://lammps.sandia.gov/threads/msg72033.html
https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
oplsaa-erg_ff
https://bitbucket.org/comcon1/oplsaa-erg_ff/src/default/
Dihedral Coeffs
https://lammps.sandia.gov/threads/msg32415.html
Moltemplate OPLS-AA improper parameters
https://lammps.sandia.gov/threads/msg72033.html
2020年3月10日 星期二
2019年11月8日 星期五
2019年10月5日 星期六
Develop/integrate molecular modeling algorithms in SAMSON with the SAMSON SDK (C++/Qt)
Installation guide
https://documentation.samson-connect.net/users/latest/user_guide_getting_started.html#InstallingSAMSON
Quick start guide
https://documentation.samson-connect.net/wp-content/uploads/SAMSON-Quick-Start-Guide.pdf
User guide
https://documentation.samson-connect.net/users/latest/
Scripting guide
https://documentation.samson-connect.net/scripting-guide/
Documentation center
https://documentation.samson-connect.net
Forum
https://documentation.samson-connect.net/users/latest/user_guide_getting_started.html#InstallingSAMSON
Quick start guide
https://documentation.samson-connect.net/wp-content/uploads/SAMSON-Quick-Start-Guide.pdf
User guide
https://documentation.samson-connect.net/users/latest/
Scripting guide
https://documentation.samson-connect.net/scripting-guide/
Documentation center
https://documentation.samson-connect.net
Forum
2019年10月4日 星期五
2019年9月25日 星期三
2019年9月10日 星期二
A reactive force field implementation in LAMMPS
LAMMPS在reax範例中的input腳本(in.CHO)
https://github.com/lammps/lammps/blob/master/examples/reax/CHO/in.CHO
其中data檔(data.CHO)為
https://github.com/lammps/lammps/blob/master/examples/reax/CHO/data.CHO
reax的建模需要注意的是units選取real，atom_style為charge
讀取模型的數據文件，可以嘗試用MS輸出car格式，利用LAMMPS中的msi2lmp工具轉化為所需的數據文件
接著選取potential類型，注意pair_style和pair_coeff應在read_data或create_box後
上述命令中lmp_control為控製文件，用於控制輸出軌跡文件trj，若無需要可將其替換為NULL
ffield.reax.cho存放在Lammps的potential資料夾
https://github.com/lammps/lammps/tree/master/potentials
，在使用其他系統時，可以選用ADF軟件中的potential文件(可以直接使用)。
對於reax的分子動力學模擬，必須有電荷守恆條件(fix qeq / reax)，其中param.qeq存放所需原子的參數，從左到右分別為原子類型，電負性(eV)，自庫倫勢，軌道指數
上述數值也存在於potential文件中，因此可以將param.qeq替換為REAX/ C，如下圖所示：
其次在進行模擬時，一般可以選用NVT，如果系統分子個數比較少，應增大溫度加快反應進程（去掉fix 1和fix 3改為）
reax的分子動力學模擬，time step應在0.1-1.0之間，一般選取0.25
執行後若要製作動畫，應生成dump文件
畫圖檔指令
topo readlammpsdata data.CHO charge
https://github.com/lammps/lammps/blob/master/examples/reax/CHO/in.CHO
# REAX potential for CHO system
# .....
units real
atom_style charge
read_data data.CHO
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.cho H C O
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.cho
run 3000其中data檔(data.CHO)為
https://github.com/lammps/lammps/blob/master/examples/reax/CHO/data.CHO
# CHO example
105 atoms
3 atom types
0 25.000 xlo xhi
0 25.000 ylo yhi
0 25.000 zlo zhi
Masses
1 1.0080
2 12.0107
3 15.9994
Atoms
1 2 0.0 10.67229 14.36836 12.47166
2 1 0.0 11.02446 14.91550 13.35233
3 1 0.0 11.02446 14.91549 11.59096
4 1 0.0 9.57932 14.41980 12.47166
5 2 0.0 11.17534 12.87608 12.47165
6 1 0.0 10.79792 12.33546 13.34037
7 1 0.0 10.79790 12.33545 11.60294
8 2 0.0 12.75013 12.93134 12.47163
9 1 0.0 13.13241 13.47175 11.60486
10 1 0.0 13.13241 13.47210 13.33818
11 2 0.0 13.22294 11.42815 12.47199
12 1 0.0 12.83858 10.89166 11.60377
13 1 0.0 12.83959 10.89255 13.34119
14 2 0.0 14.79762 11.45137 12.47107
15 1 0.0 15.21044 10.43808 12.47354
16 1 0.0 15.19550 11.96345 11.58877
17 1 0.0 15.19648 11.96815 13.35018
18 2 0.0 0.24250 0.91354 1.10383
19 1 0.0 0.97225 1.67509 1.39797
20 1 0.0 24.87363 1.18825 0.11010
21 1 0.0 24.39847 0.98637 1.79630
22 2 0.0 0.86944 24.46895 1.11508
23 1 0.0 1.21047 24.19771 2.11484
24 1 0.0 0.12679 23.71752 0.84453
25 2 0.0 2.06454 24.48829 0.08825
26 1 0.0 1.72846 24.75977 24.08683
27 1 0.0 2.80951 0.23920 0.35408
28 2 0.0 2.67036 23.03401 0.12171
29 1 0.0 1.92204 22.28680 24.85503
30 1 0.0 3.00638 22.76782 1.12450
31 2 0.0 3.87027 23.02208 24.10132
32 1 0.0 4.35176 22.04072 24.06515
33 1 0.0 3.54082 23.26189 23.08511
34 1 0.0 4.63935 23.75310 24.37121
35 2 0.0 1.37929 14.62909 17.52744
36 1 0.0 1.08393 15.52196 18.08818
37 1 0.0 2.47385 14.59977 17.52258
38 1 0.0 1.05260 14.77122 16.49293
39 2 0.0 0.76275 13.31937 18.14786
40 1 0.0 24.67295 13.35030 18.12450
41 1 0.0 1.04396 12.44064 17.56651
42 2 0.0 1.30113 13.22425 19.62581
43 1 0.0 2.39107 13.19385 19.65447
44 1 0.0 1.02336 14.10169 20.21106
45 2 0.0 0.66878 11.90830 20.21883
46 1 0.0 0.94960 11.03396 19.63080
47 1 0.0 24.57945 11.94426 20.18968
48 2 0.0 1.19125 11.78568 21.69954
49 1 0.0 0.79365 10.89123 22.18875
50 1 0.0 2.28374 11.72162 21.74071
51 1 0.0 0.89616 12.64769 22.30679
52 2 0.0 11.41750 7.16471 22.76002
53 1 0.0 11.74866 7.28340 21.72336
54 1 0.0 11.72154 8.06612 23.30055
55 1 0.0 11.97469 6.32478 23.18558
56 2 0.0 9.86319 6.92474 22.85179
57 1 0.0 9.57626 6.01094 22.33031
58 1 0.0 9.54930 6.78307 23.88660
59 2 0.0 9.17390 8.18942 22.21244
60 1 0.0 9.45849 9.10599 22.73021
61 1 0.0 9.48557 8.33580 21.17777
62 2 0.0 7.62459 7.92132 22.31840
63 1 0.0 7.31756 7.77569 23.35472
64 1 0.0 7.34468 7.00469 21.79795
65 2 0.0 6.90692 9.17258 21.68631
66 1 0.0 5.81845 9.06496 21.71809
67 1 0.0 7.15914 10.09632 22.21721
68 1 0.0 7.18992 9.31630 20.63835
69 2 0.0 4.69047 14.13340 23.48572
70 1 0.0 4.95366 15.17281 23.26391
71 1 0.0 5.39163 13.78010 24.24888
72 1 0.0 4.87514 13.55000 22.57874
73 2 0.0 3.19477 13.99798 23.95930
74 1 0.0 2.50599 14.33002 23.18163
75 1 0.0 2.93803 12.95591 24.15345
76 2 0.0 3.05322 14.87431 0.26136
77 1 0.0 3.74058 14.54651 1.04202
78 1 0.0 3.30993 15.91730 0.07257
79 2 0.0 1.55058 14.71961 0.71013
80 1 0.0 1.29864 13.67531 0.89801
81 1 0.0 0.86725 15.05003 24.92701
82 2 0.0 1.37850 15.58633 2.01380
83 1 0.0 0.35341 15.53527 2.39297
84 1 0.0 2.04062 15.24695 2.81709
85 1 0.0 1.60704 16.64178 1.83261
86 3 0.0 8.51658 13.05007 22.43728
87 3 0.0 9.43965 13.72051 21.88842
88 3 0.0 18.16518 4.73455 8.81928
89 3 0.0 18.65469 4.57291 7.66370
90 3 0.0 6.43553 20.34119 24.80049
91 3 0.0 6.44898 20.31621 23.53493
92 3 0.0 21.90539 11.54301 19.82384
93 3 0.0 20.76137 11.61918 20.36007
94 3 0.0 3.42232 11.07545 5.77130
95 3 0.0 3.88671 10.95299 4.60048
96 3 0.0 11.93988 4.94134 20.86058
97 3 0.0 12.98804 5.47798 20.39555
98 3 0.0 14.08646 9.50799 20.80806
99 3 0.0 14.09449 10.68237 20.33642
100 3 0.0 3.45246 19.93144 16.38965
101 3 0.0 2.86282 19.60263 15.31936
102 3 0.0 12.85008 21.95287 13.63796
103 3 0.0 12.06593 21.16486 14.24238
104 3 0.0 24.47055 7.42219 14.24997
105 3 0.0 24.43181 7.37102 12.98624reax的建模需要注意的是units選取real，atom_style為charge
units real
atom_style charge讀取模型的數據文件，可以嘗試用MS輸出car格式，利用LAMMPS中的msi2lmp工具轉化為所需的數據文件
read_data data.CHO接著選取potential類型，注意pair_style和pair_coeff應在read_data或create_box後
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.cho H C O
neighbor 2 bin
neigh_modify every 10 delay 0 check no上述命令中lmp_control為控製文件，用於控制輸出軌跡文件trj，若無需要可將其替換為NULL
ffield.reax.cho存放在Lammps的potential資料夾
https://github.com/lammps/lammps/tree/master/potentials
，在使用其他系統時，可以選用ADF軟件中的potential文件(可以直接使用)。
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0對於reax的分子動力學模擬，必須有電荷守恆條件(fix qeq / reax)，其中param.qeq存放所需原子的參數，從左到右分別為原子類型，電負性(eV)，自庫倫勢，軌道指數
1 5.3200 14.8732 1.0206
2 5.8678 14.0000 0.9000
3 8.5000 17.9978 1.0503上述數值也存在於potential文件中，因此可以將param.qeq替換為REAX/ C，如下圖所示：
其次在進行模擬時，一般可以選用NVT，如果系統分子個數比較少，應增大溫度加快反應進程（去掉fix 1和fix 3改為）
fix 1 all nvt temp 3500.0 3500.0 100.0
timestep 0.25執行後若要製作動畫，應生成dump文件
dump 1 all custom mass type xs ys zs fx fy fz畫圖檔指令
topo readlammpsdata data.CHO charge
2019年5月3日 星期五
2019年4月21日 星期日
Python libraries for Chemistry
scikit-chem (https://github.com/richlewis42/scikit-chem) and RDKit (https://github.com/rdkit/rdkit)提供了一組Python library用於設計化學分析工作流程、預測常見功能以及在數據格式之間進行轉換。
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