sobereva 发表于 2023-3-17 15:17 好的，谢谢老师 |
| 还是用DFT吧。这体系不大，跑起来很快。即便用半经验级别的方法跑出来的现象符合预期，也可能会遭质疑 |
sobereva 发表于 2023-3-17 14:39 好的老师以后注意。我用GFN1-xTB跑过了，在结构优化完就出现这样的问题了，而用DFTB结构优化完是没问题的，在跑完NVT动力学后出现这样的问题。 |
sobereva 发表于 2023-3-17 14:31 键是羟胺基上的N-H键在跑完后键长变的更长了 |
joke122 发表于 2023-3-17 14:35 以后输入文件作为附件上传 输入文件本身没明显问题，注意我前面说的其它问题。并且可以尝试用GFN1-xTB。如果GFN1-xTB结果也怪，直接用DFT跑。本身这种环氮类体系用半经验级别的方法就未必能描述得当。 |
sobereva 发表于 2023-3-17 14:31 抱歉老师，我的输入文件发错了，以下是我的输入文件 #Generated by Multiwfn &GLOBAL PROJECT N516zhengchangjiegou PRINT_LEVEL LOW RUN_TYPE MD PREFERRED_DIAG_LIBRARY SL &END GLOBAL &FORCE_EVAL METHOD Quickstep &SUBSYS &CELL A 16.89800000 0.00000000 0.00000000 B 0.00000000 14.36000000 0.00000000 C 0.38488733 0.00000000 6.77808105 PERIODIC XYZ #Direction of applied PBC (geometry aspect) &END CELL &COORD N 1.61400000 5.38800000 4.92300000 N 2.45300000 6.25000000 5.50400000 N 3.27500000 5.54900000 6.30300000 N 2.93800000 4.25900000 6.21500000 N 1.91400000 4.16000000 5.36600000 N 0.62600000 5.65400000 1.66400000 H 1.40400000 6.38500000 1.63900000 H 0.02000000 5.75700000 0.78400000 H 1.03300000 4.64200000 1.69800000 O -0.21800000 5.87600000 2.77000000 H 0.29900000 5.66800000 3.63500000 N 3.18700000 12.56800000 5.24400000 N 2.34800000 13.43000000 4.66200000 N 1.52700000 12.72900000 3.86400000 N 1.86300000 11.43900000 3.95300000 N 2.88700000 11.34000000 4.80200000 N 3.79000000 12.83500000 1.72500000 H 3.01200000 13.56600000 1.74900000 H 4.39600000 12.93700000 2.60500000 H 3.38500000 11.82200000 1.68900000 O 4.63500000 13.05600000 0.61900000 H 4.11700000 12.84900000 -0.24500000 N 2.99500000 8.97300000 1.85500000 N 2.15600000 8.11100000 1.27400000 N 1.33500000 8.81100000 0.47500000 N 1.67100000 10.10100000 0.56300000 N 2.69500000 10.20100000 1.41200000 N 3.98200000 8.70600000 5.11400000 H 3.20400000 7.97400000 5.13900000 H 4.58800000 8.60400000 5.99300000 H 3.57600000 9.71900000 5.07900000 O 4.82600000 8.48400000 4.00800000 H 4.30900000 8.69200000 3.14300000 N 1.42200000 1.79200000 1.53400000 N 2.26100000 0.93000000 2.11600000 N 3.08300000 1.63200000 2.91400000 N 2.74600000 2.92200000 2.82500000 N 1.72200000 3.02000000 1.97500000 N 0.81800000 1.52600000 5.05200000 H 1.59600000 0.79500000 5.02900000 H 0.21300000 1.42300000 4.17200000 H 1.22400000 2.53900000 5.08800000 O -0.02700000 1.30500000 6.15900000 H 0.49100000 1.51200000 7.02300000 N 5.84000000 5.38800000 4.92300000 N 6.67900000 6.25000000 5.50500000 N 7.50000000 5.54800000 6.30400000 N 7.16300000 4.25900000 6.21600000 N 6.13900000 4.16000000 5.36600000 N 4.85000000 5.65400000 1.66300000 H 5.62700000 6.38500000 1.63900000 H 4.24300000 5.75600000 0.78400000 H 5.25700000 4.64100000 1.69800000 O 4.00700000 5.87500000 2.77100000 H 4.52700000 5.66900000 3.63400000 N 7.41000000 12.56900000 5.24400000 N 6.57100000 13.43000000 4.66200000 N 5.75100000 12.72800000 3.86300000 N 6.08800000 11.43900000 3.95200000 N 7.11100000 11.34000000 4.80200000 N 8.01500000 12.83400000 1.72600000 H 7.23700000 13.56500000 1.75100000 H 8.62300000 12.93600000 2.60300000 H 7.60800000 11.82100000 1.69200000 O 8.85800000 13.05500000 0.61900000 H 8.33900000 12.85100000 -0.24600000 N 7.21900000 8.97300000 1.85500000 N 6.37900000 8.11100000 1.27400000 N 5.55800000 8.81200000 0.47500000 N 5.89500000 10.10200000 0.56200000 N 6.91900000 10.20100000 1.41200000 N 8.20700000 8.70700000 5.11500000 H 7.42900000 7.97500000 5.14100000 H 8.81600000 8.60400000 5.99200000 H 7.80000000 9.71900000 5.08100000 O 9.05000000 8.48600000 4.00700000 H 8.53100000 8.69000000 3.14300000 N 5.64700000 1.79200000 1.53500000 N 6.48700000 0.93100000 2.11700000 N 7.30700000 1.63200000 2.91500000 N 6.97100000 2.92200000 2.82600000 N 5.94700000 3.02100000 1.97600000 N 5.04200000 1.52600000 5.05200000 H 5.82000000 0.79500000 5.02700000 H 4.43500000 1.42400000 4.17300000 H 5.44800000 2.53900000 5.08700000 O 4.19900000 1.30600000 6.15900000 H 4.71800000 1.51100000 7.02300000 N 10.06500000 5.38800000 4.92300000 N 10.90500000 6.25000000 5.50400000 N 11.72500000 5.54900000 6.30400000 N 11.38800000 4.25900000 6.21600000 N 10.36500000 4.16000000 5.36600000 N 9.07600000 5.65300000 1.66300000 H 9.85400000 6.38500000 1.63700000 H 8.46800000 5.75600000 0.78500000 H 9.48400000 4.64100000 1.69700000 O 8.23400000 5.87600000 2.77100000 H 8.75200000 5.67000000 3.63500000 N 11.63600000 12.56900000 5.24300000 N 10.79700000 13.43000000 4.66200000 N 9.97600000 12.72800000 3.86300000 N 10.31300000 11.43800000 3.95200000 N 11.33700000 11.34000000 4.80200000 N 12.24100000 12.83400000 1.72600000 H 11.46300000 13.56500000 1.75100000 H 12.84800000 12.93700000 2.60400000 H 11.83400000 11.82100000 1.69200000 O 13.08400000 13.05400000 0.61900000 H 12.56600000 12.85000000 -0.24500000 N 11.44400000 8.97300000 1.85500000 N 10.60400000 8.11100000 1.27400000 N 9.78400000 8.81200000 0.47500000 N 10.12100000 10.10200000 0.56200000 N 11.14400000 10.20100000 1.41200000 N 12.43300000 8.70600000 5.11500000 H 11.65600000 7.97500000 5.14100000 H 13.04100000 8.60400000 5.99300000 H 12.02600000 9.71900000 5.08100000 O 13.27600000 8.48500000 4.00800000 H 12.75700000 8.69100000 3.14400000 N 9.87300000 1.79100000 1.53500000 N 10.71200000 0.93000000 2.11700000 N 11.53300000 1.63200000 2.91500000 N 11.19600000 2.92200000 2.82600000 N 10.17200000 3.02000000 1.97600000 N 9.26900000 1.52600000 5.05200000 H 10.04700000 0.79500000 5.02700000 H 8.66100000 1.42400000 4.17300000 H 9.67500000 2.53900000 5.08700000 O 8.42500000 1.30500000 6.15900000 H 8.94400000 1.51000000 7.02300000 N 14.28800000 5.38700000 4.92400000 N 15.12700000 6.25000000 5.50400000 N 15.94900000 5.54900000 6.30300000 N 15.61300000 4.25900000 6.21500000 N 14.58900000 4.15900000 5.36600000 N 13.30100000 5.65400000 1.66400000 H 14.07900000 6.38500000 1.63900000 H 12.69600000 5.75700000 0.78400000 H 13.70800000 4.64200000 1.69800000 O 12.45700000 5.87600000 2.77000000 H 12.97400000 5.66900000 3.63500000 N 15.86200000 12.56800000 5.24400000 N 15.02300000 13.43000000 4.66200000 N 14.20100000 12.72800000 3.86400000 N 14.53700000 11.43900000 3.95300000 N 15.56100000 11.34000000 4.80200000 N 16.46500000 12.83500000 1.72600000 H 15.68700000 13.56600000 1.74900000 H 17.07000000 12.93700000 2.60500000 H 16.05900000 11.82200000 1.69000000 O 17.31000000 13.05500000 0.62000000 H 16.79300000 12.84900000 -0.24500000 N 15.67000000 8.97300000 1.85500000 N 14.83000000 8.11100000 1.27400000 N 14.00900000 8.81100000 0.47500000 N 14.34500000 10.10100000 0.56300000 N 15.36900000 10.20100000 1.41200000 N 16.65700000 8.70600000 5.11500000 H 15.87900000 7.97400000 5.13900000 H 17.26300000 8.60300000 5.99400000 H 16.25100000 9.71900000 5.08000000 O 17.50200000 8.48500000 4.00900000 H 16.98500000 8.69200000 3.14400000 N 14.09700000 1.79200000 1.53500000 N 14.93600000 0.93000000 2.11600000 N 15.75700000 1.63200000 2.91400000 N 15.42100000 2.92200000 2.82600000 N 14.39700000 3.02000000 1.97600000 N 13.49300000 1.52600000 5.05200000 H 14.27100000 0.79500000 5.02900000 H 12.88800000 1.42300000 4.17200000 H 13.89900000 2.53900000 5.08800000 O 12.64900000 1.30400000 6.15800000 H 13.16600000 1.51100000 7.02300000 &END COORD # &VELOCITY #You can set initial atomic velocities in this section # &END VELOCITY &END SUBSYS &DFT # WFN_RESTART_FILE_NAME N516zhengchangjiegou-RESTART.wfn CHARGE 0 #Net charge MULTIPLICITY 1 #Spin multiplicity &QS EPS_DEFAULT 1.0E-10 #Set all EPS_xxx to values such that the energy will be correct up to this value EXTRAPOLATION ASPC #Extrapolation for wavefunction during e.g. MD. ASPC is default, PS also be used EXTRAPOLATION_ORDER 3 #Order for PS or ASPC extrapolation. 3 is default METHOD DFTB &DFTB SELF_CONSISTENT T DO_EWALD T DISPERSION T DIAGONAL_DFTB3 T HB_SR_GAMMA T &PARAMETER PARAM_FILE_PATH DFTB/scc PARAM_FILE_NAME scc_parameter UFF_FORCE_FIELD ../uff_table HB_SR_PARAM 4 &END PARAMETER &END DFTB &END QS &POISSON &EWALD EWALD_TYPE SPME GMAX 34 28 14 &END EWALD &END POISSON &SCF MAX_SCF 125 #Maximum number of steps of inner SCF EPS_SCF 1.0E-05 #Convergence threshold of density matrix of inner SCF # SCF_GUESS RESTART #Use wavefunction from WFN_RESTART_FILE_NAME file as initial guess &OT PRECONDITIONER FULL_SINGLE_INVERSE MINIMIZER DIIS #CG is worth to consider in difficult cases LINESEARCH 2PNT #1D line search algorithm for CG. 2PNT is default, 3PNT is better but more costly. GOLD is best but very expensive &END OT &OUTER_SCF MAX_SCF 20 #Maximum number of steps of outer SCF EPS_SCF 1.0E-05 #Convergence threshold of outer SCF &END OUTER_SCF &RESTART OFF #Do not generate wfn file to suppress meaningless I/O cost &END RESTART &END PRINT &END SCF &END DFT &END FORCE_EVAL &MOTION &MD ENSEMBLE NVT STEPS 2000 #Number of steps to run TIMESTEP 0.25 #Step size in fs. Decrease it properly for high temperature simulation TEMPERATURE 298.15 #Initial and maintained temperature (K) # COMVEL_TOL 0 #Uncomment this can remove translation motion of center-of-mass every step &THERMOSTAT TYPE NOSE &END THERMOSTAT &PROGRAM_RUN_INFO &EACH MD 1 #Output frequency of MD information, 0 means never &END EACH &END PROGRAM_RUN_INFO &END PRINT &END MD &TRAJECTORY &EACH MD 1 #Output frequency of coordinates, 0 means never &END EACH FORMAT pdb &END TRAJECTORY &VELOCITIES &EACH MD 0 #Output frequency of velocities, 0 means never &END EACH &END VELOCITIES &FORCES &EACH MD 0 #Output frequency of forces, 0 means never &END EACH &END FORCES &RESTART BACKUP_COPIES 0 #Maximum number of backing up restart file, 0 means never &EACH MD 1 #Frequency of updating last restart file, 0 means never &END EACH &END RESTART &RESTART_HISTORY OFF &END RESTART_HISTORY &END PRINT &END MOTION |
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没输入文件没法说 而且也不知道你说的键具体是什么键 此体系Z方向尺寸太短，MD没意义 |
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