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标题: 求助用CP2K中的DFTB跑NVT后分子结构改变 [打印本页]

作者
Author: joke122 时间: 2023-3-17 14:09
标题: 求助用CP2K中的DFTB跑NVT后分子结构改变
各位老师好
我在使用CP2K中的DFTB跑NVT动力学，发现结构的其中一个分子键在跑完后发生改变，请问我这是DFTB参数缺少还是体系不适用？我的CP2K输入inp文件是通过multiwfn产生，然后再自己添加的参数。
以下是我的输入文件和输出结构

作者
Author: sobereva 时间: 2023-3-17 14:31
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

作者
Author: joke122 时间: 2023-3-17 14:35

sobereva 发表于 2023-3-17 14:31
没输入文件没法说

而且也不知道你说的键具体是什么键

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
   &PRINT
      &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
&PRINT
   &PROGRAM_RUN_INFO
      &EACH
      MD    1 #Output frequency of MD information, 0 means never
      &END EACH
   &END PROGRAM_RUN_INFO
&END PRINT
  &END MD
  &PRINT
&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

作者
Author: sobereva 时间: 2023-3-17 14:39

joke122 发表于 2023-3-17 14:35
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

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。

作者
Author: joke122 时间: 2023-3-17 14:40

sobereva 发表于 2023-3-17 14:31
没输入文件没法说

而且也不知道你说的键具体是什么键

键是羟胺基上的N-H键在跑完后键长变的更长了

作者
Author: joke122 时间: 2023-3-17 14:43

sobereva 发表于 2023-3-17 14:39
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 ...

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。

作者
Author: sobereva 时间: 2023-3-17 15:17
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

作者
Author: joke122 时间: 2023-3-17 15:22

sobereva 发表于 2023-3-17 15:17
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

好的，谢谢老师

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