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yangxinyeah銅蟲(chóng) (小有名氣)
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[求助]
在Towhee中用TraPPE-EH力場(chǎng)模擬benzene的VLE曲線 已有1人參與
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大家好： 最近我用Towhee軟件在模擬苯的氣液平衡數(shù)據(jù)時(shí)發(fā)現(xiàn)只能選擇TraPPE-UA力場(chǎng)。TraPPE-EH力場(chǎng)中只定義了CO2和N2。所以我在參數(shù)文件中把Siepmann的苯的TraPPE-EH力場(chǎng)數(shù)據(jù)增加進(jìn)去。并且在input文件中也定義了苯的鏈接信息。但是程序報(bào)錯(cuò)，請(qǐng)問(wèn)論壇里哪位高手知道這個(gè)怎么解決嗎？小女子在此拜謝了。還請(qǐng)大家?guī)臀野伞?br /> 報(bào)錯(cuò)信息為： input_style: advanced connectivity map nunit: 12 nmaxcbmc: 12 lpdbnames: F using the TraPPE-EH force field charge_assignment: bond increment improper_assignment: none match_style: standard Building the input file for molecule type: 1 unit: 1 name:Caro Mismatch of strings in buildmolec Expected String: unit Found String: impr Fatal error, quitting. 我的輸入文件： inputformat 'Towhee' ensemble 'nvt' temperature 520.0d0 nmolty 1 nmolectyp 250 numboxes 2 stepstyle 'cycles' nstep 20000 printfreq 2000 blocksize 4000 moviefreq 4000 backupfreq 4000 runoutput 'full' pdb_output_freq 4000 loutdft .false. loutlammps .false. loutdlpoly .false. pressurefreq 10 trmaxdispfreq 200 volmaxdispfreq 200 potentialstyle 'internal' ffnumber 1 ff_filename /home/liuxd/towhee-7.1.0/ForceFields/towhee_ff_TraPPE-EH classical_potential 'Lennard-Jones' classical_mixrule 'Lorentz-Berthelot' lshift .false. ltailc .true. rmin 0.6d0 rcut 14.0d0 rcutin 10.0d0 electrostatic_form 'coulomb' coulombstyle 'ewald_fixed_kmax' kalp 5.6d0 kmax 8 dielect 1.0d0 linit .true. initboxtype 'dimensions' initstyle 'full cbmc' 'full cbmc' initlattice 'simple cubic' 'simple cubic' initmol 210 40 inix iniy iniz 8 8 7 4 4 4 hmatrix 30.0d0 0.0d0 0.0d0 0.0d0 30.0d0 0.0d0 0.0d0 0.0d0 30.0d0 60.d0 0.0d0 0.0d0 0.0d0 60.d0 0.0d0 0.0d0 0.0d0 60.d0 pmvol 0.002d0 pmvlpr 1.0d0 rmvol 0.1d0 tavol 0.5d0 pmcell 0.0d0 pmcellpr 1.0d0 pmcellpt 0.5d0 rmcell 1.0d0 tacell 0.5d0 pm2boxrbswap 0.0d0 pm2rbswmt 1.0d0 pm2rbswpr 1.0d0 pm2boxcbswap 0.01d0 pm2cbswmt 1.0d0 pm2cbswpr 1.0d0 pm1boxcbswap 0.0d0 pm1cbswmt 1.0d0 pmcb 0.4d0 pmcbmt 1.0d0 pmall 0.0d0 pmtracm 0.7d0 pmtcmt 1.0d0 rmtrac 0.5d0 tatrac 0.5d0 pmrotate 1.0d0 pmromt 1.0d0 rmrot 0.05d0 tarot 0.5d0 cbmc_formulation 'Martin and Frischknecht 2006' cbmc_setting_style 'Martin and Frischknecht' #trappe-EH benzene input_style 'advanced connectivity map' nunit 12 nmaxcbmc 12 lpdbnames F forcefield 'TraPPE-EH' charge_assignment 'bond increment' improper_assignment 'none' match_style 'standard' unit ntype 1 'Caro' vibration 3 2 'aromatic' 6 'aromatic' 7 'single' improper torsion 0 unit ntype 2 'Caro' vibration 3 1 'aromatic' 3 'aromatic' 8 'single' improper torsion 0 unit ntype 3 'Caro' vibration 3 2 'aromatic' 4 'aromatic' 9 'single' improper torsion 0 unit ntype 4 'Caro' vibration 3 3 'aromatic' 5 'aromatic' 10 'single' improper torsion 0 unit ntype 5 'Caro' vibration 3 4 'aromatic' 6 'aromatic' 11 'single' improper torsion 0 unit ntype 6 'Caro' vibration 3 5 'aromatic' 1 'aromatic' 12 'single' improper torsion 0 unit ntype 7 'Haro' vibration 1 1 'single' improper torsion 0 unit ntype 8 'Haro' vibration 1 2 'single' improper torsion 0 unit ntype 9 'Haro' vibration 1 3 'single' improper torsion 0 unit ntype 10 'Haro' vibration 1 4 'single' improper torsion 0 unit ntype 11 'Haro' vibration 1 5 'single' improper torsion 0 unit ntype 12 'Haro' vibration 1 6 'single' improper torsion 0 修改后的力場(chǎng)文件： towhee_ff Version 15 Number of Nonbonded Types 6 Potential Type Lennard-Jones Classical Mixrule Lorentz-Berthelot Atom Type Number 1 Nonbond Coefficients 0.2800000000E+01 0.2700000000E+02 0.0000000000E+00 0.0000000000E+00 Mass 0.1201100000E+02 Element C Bond Pattern null Base Charge 0.0000000000E+00 Polarizability 0.1000000000E+01 Force Field Name TraPPE-EH Atom Names C_co2 C_co2 C_co2 none Atom Type Number 2 Nonbond Coefficients 0.3050000000E+01 0.7900000000E+02 0.0000000000E+00 0.0000000000E+00 Mass 0.1599900000E+02 Element O Bond Pattern null Base Charge 0.0000000000E+00 Polarizability 0.1000000000E+01 Force Field Name TraPPE-EH Atom Names O_co2 O_co2 O_co2 none Atom Type Number 3 Nonbond Coefficients 0.3310000000E+01 0.3600000000E+02 0.0000000000E+00 0.0000000000E+00 Mass 0.1400700000E+02 Element N Bond Pattern null Base Charge 0.0000000000E+00 Polarizability 0.1000000000E+01 Force Field Name TraPPE-EH Atom Names N_n2 N_n2 N_n2 none Atom Type Number 4 Nonbond Coefficients 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 Mass 0.0000000000E+00 Element - Bond Pattern null Base Charge 0.0000000000E+00 Polarizability 0.1000000000E+01 Force Field Name TraPPE-EH Atom Names COM_n2 COM_n2 COM_n2 none Atom Type Number 5 Nonbond Coefficients 0.3600000000E+01 0.3070000000E+02 0.0000000000E+00 0.0000000000E+00 Mass 0.1201100000E+02 Element C Bond Pattern null Base Charge 0.0000000000E+00 Polarizability 0.1000000000E+01 Force Field Name TraPPE-EH Atom Names Caro Caro Caro none Atom Type Number 6 Nonbond Coefficients 0.2360000000E+01 0.2545000000E+02 0.0000000000E+00 0.0000000000E+00 Mass 0.1007900000E+01 Element H Bond Pattern null Base Charge 0.0000000000E+00 Polarizability 0.1000000000E+01 Force Field Name TraPPE-EH Atom Names Haro Haro Haro none Number of Bonded Terms 4 Bond Type Number 1 Bond Style 1 Bond Coefficients 0.1160000000E+01 Vibration Order wild Force Field Name TraPPE-EH Number of Atoms with Same Parameters 1 Atom Names C_co2 O_co2 Bond Type Number 2 Bond Style 1 Bond Coefficients 0.5500000000E+00 Vibration Order wild Force Field Name TraPPE-EH Number of Atoms with Same Parameters 1 Atom Names N_n2 COM_n2 Bond Type Number 3 Bond Style 1 Bond Coefficients 0.1080000000E+01 Vibration Order wild Force Field Name TraPPE-EH Number of Atoms with Same Parameters 1 Atom Names Caro Haro Bond Type Number 4 Bond Style 1 Bond Coefficients 0.1392000000E+01 Vibration Order wild Force Field Name TraPPE-EH Number of Atoms with Same Parameters 1 Atom Names Caro Caro Number of Angle Terms 2 Angle Type Number 1 Angle Style 0 Angle Coefficients 0.1800000000E+03 0.1000000000E-04 Angle Order wild Force Field Name TraPPE-EH Number of Atoms with Same Parameters 2 Atom Names O_co2 C_co2 O_co2 N_n2 COM_n2 N_n2 Angle Type Number 2 Angle Style 0 Angle Coefficients 0.1200000000E+03 0.1000000000E-04 Angle Order wild Force Field Name TraPPE-EH Number of Atoms with Same Parameters 3 Atom Names Caro Caro Caro Haro Caro Haro Caro Caro Haro Number of Torsion Terms 0 Number of Improper Terms 0 Number of Angle-Angle Terms 0 Number of One-Five Types 0 Number of Bond Increments 4 Bond Increment Type Number 1 Bond Increment Value -0.3500000000E+00 Bond Increment Order wild Force Field Name TraPPE-EH Atom Names O_co2 C_co2 Bond Increment Type Number 2 Bond Increment Value -0.4820000000E+00 Bond Increment Order wild Force Field Name TraPPE-EH Atom Names N_n2 COM_n2 Bond Increment Type Number 3 Bond Increment Value 0.0000000000E+00 Bond Increment Order wild Force Field Name TraPPE-UA Atom Names Caro Caro Bond Increment Type Number 4 Bond Increment Value -0.9500000000E+00 Bond Increment Order wild Force Field Name TraPPE-UA Atom Names Caro Haro |
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yangxinyeah
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2樓2016-04-22 07:05:40
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3樓2016-04-22 11:41:20
【答案】應(yīng)助回帖
感謝參與，應(yīng)助指數(shù) +1
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把所有的 improper torsion 0 去掉。 好好看看教程中關(guān)于improper_assignment=none的情況 http://towhee.sourceforge.net/in ... improper_assignment |
4樓2016-04-23 16:17:33
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5樓2016-04-25 15:31:24
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