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【求助】DL_POLY的config文件如何生成?? 已有9人参与
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我想模拟聚合物在金属团簇表面的吸附,想请教大家这样的体系的config文件如何生成? 另外我把手册已经看了一遍,但是希望运行一下.有么有人根据手册的算例给写一个模拟过程,给传一个谢谢!! |
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64楼2010-03-27 14:33:36
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您好,我的体系是40个正丁硫醇体系,用dl_poly3.09版本,已经运行了100步停止了,出现这样的错误提示: error - r_14 > rcut in dihedrals_forces 我的CONTROL是这样的 DL_POLY TEST CASE integrator leapfrog verlet temperature 300.00 pressure 0.0000 ensemble nvt berendesen 0.1 no index steps 10000 multiple step 1 scale 10 print 50 stack 100 stats 10 traj 1000 100 0 densvar 30 timestep 0.00010 cutoff 12.0000 delr width 1.0000 rvdw cutoff 10.0000 no electrostatics quaternion tolerance 1.0E-5 job time 18000.00 close time 300.00 finish 然后我就根据error提示,把cutoff改为13.000 可是出现这样的错误提示: error - wrongly indexed atom entries found in CONFIG file 我检查CONFIG没有错误啊.... 望能给些意见,谢谢!! |
66楼2010-04-01 10:21:54
这是我运行了100步停止的输出文件''''''''''''
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这是我运行了100步停止的输出文件.......... ************** stfc/ccp5 program library package daresbury laboratory molecular D L _ P O L Y dynamics program for large systems authors: i.t.todorov & w.smith ************** version 3.09.4 / september 2008 ************** Execution on 8 node(s) ****** node/domain decomposition (x,y,z): 2 2 2 link-cell decomposition 1 (x,y,z): 1 1 1 warning issued 100 *** warning - employed link cell algorithm has a link cell dimension is < 4 !!! *** *** DL_POLY_3 RUNNING IN LOW EFFICIENCY MODE !!! *** ********************************************************************************************************************************** ********************************************************************************************************************************** ********************************************************************************************************************************** ************************ DL_POLY TEST CASE 2: Al with Sutton-Chen potential ************************ ********************************************************************************************************************************** ********************************************************************************************************************************** ********************************************************************************************************************************** SIMULATION CONTROL PARAMETERS simulation temperature (K) 3.0000E+02 simulation pressure (katms) 0.0000E+00 Integration : Leapfrog Verlet Ensemble : NVT Berendsen thermostat relaxation time (ps) 1.0000E-01 no index (reading in CONFIG) option on selected number of timesteps 10000 warning issued 36 *** warning - DL_POLY_2 directive 'mult(iple timestep)' defaulted to *** *** DL_POLY_3 'infrequent k-space SPME evaluation' directive *** temperature scaling on (during equilibration) temperature scaling interval 10 data printing interval 50 data stacking interval 100 statistics file interval 10 trajectory file option on trajectory file start 1000 trajectory file interval 100 trajectory file info key 0 density variation allowance (%) 3.0000E+01 real space cutoff (Ang) 1.3000E+01 warning issued 35 *** warning - redundant directive delr ignored *** vdw cutoff (Ang) 1.0000E+01 warning issued 33 *** warning - redundant directive quaternion ignored *** user allocated job time (s) 1.8000E+04 job closure time (s) 3.0000E+02 clean start requested Electrostatics switched off!!! fixed simulation timestep (ps) 1.0000E-04 data dumping interval 1000 SYSTEM SPECIFICATION energy units = kJ/mol number of molecular types 1 molecular species type 1 name of species: butanethiol number of molecules 40 number of atoms/sites 5 atomic characteristics: site name mass charge repeat freeze 1 C1 15.035000 0.000000 1 0 2 C2 14.027000 0.000000 1 0 3 C2 14.027000 0.000000 1 0 4 C2 14.027000 0.000000 1 0 5 S14 33.068000 0.000000 1 0 number of chemical bonds 4 chemical bond details: unit key index index parameters 1 harm 1 2 500000.000000 1.540000 0.000000 0.000000 2 harm 2 3 500000.000000 1.540000 0.000000 0.000000 3 harm 3 4 500000.000000 1.540000 0.000000 0.000000 4 harm 4 5 500000.000000 1.820000 0.000000 0.000000 number of bond angles 3 bond angle details: unit key index index index f-const angle 1 harm 1 2 3 0.158000 114.400000 0.000000 0.000000 2 harm 2 3 4 0.158000 114.400000 0.000000 0.000000 3 harm 3 4 5 0.158000 114.400000 0.000000 0.000000 number of dihedral angles 2 dihedral angle details: unit key index index index index f-const angle trig 1-4 elec 1-4 vdw 1 cos3 1 2 3 4 5.904600 -1.134000 13.160800 0.000000 0.000000 0.000000 0.000000 2 cos3 2 3 4 5 5.904600 -1.134000 13.160800 0.000000 0.000000 0.000000 0.000000 number of specified vdw potentials 6 pair atom 1 atom 2 key parameters 1 C1 C1 lj 0.814600 3.750000 0.000000 0.000000 0.000000 2 C2 C2 lj 0.382000 3.950000 0.000000 0.000000 0.000000 3 S14 S14 lj 1.046000 4.450000 0.000000 0.000000 0.000000 4 C1 C2 lj 0.558000 3.850000 0.000000 0.000000 0.000000 5 C1 S14 lj 0.923000 4.100000 0.000000 0.000000 0.000000 6 C2 S14 lj 0.633000 4.200000 0.000000 0.000000 0.000000 configuration file name: input-turn-config selected image convention 1 simulation cell vectors 30.0000000000 0.0000000000 0.0000000000 0.0000000000 30.0000000000 0.0000000000 0.0000000000 0.0000000000 30.0000000000 system volume 27000.0000000 long-range correction for: vdw energy -0.317042E+02 : vdw pressure -0.384247E-01 degrees of freedom break-down list ---------------------------------- all particles 600 centre of mass -3 non-periodicity 0 frozen 0 shell-pseudo 0 constrained 0 ---------------------------------- total (real) 597 sample of starting configuration on node zero i x(i) y(i) z(i) vx(i) vy(i) vz(i) 1 -5.3460E+00 -4.3530E+00 -5.8400E+00 5.3187E+00 1.6975E+00 -3.5250E+00 3 -6.9280E+00 -5.8680E+00 -7.2810E+00 4.2182E+00 2.1674E+00 -2.8500E+00 5 -4.4550E+00 -2.7160E+00 -5.8810E+00 -5.2572E+00 -2.0707E-01 2.9524E+00 14 -1.6820E+00 -9.4200E-01 -2.2340E+00 6.7830E+00 1.7340E-01 -6.5509E+00 71 -7.3000E-01 -3.3240E+00 -6.1350E+00 -4.3704E+00 -3.9108E-01 -3.1877E+00 73 -4.1200E-01 -5.9120E+00 -5.8400E+00 3.1470E-01 -4.4419E+00 1.7874E-03 141 -7.2950E+00 -2.7620E+00 -1.3680E+00 1.6247E+00 5.0967E+00 -2.4214E+00 143 -9.5090E+00 -1.8080E+00 -2.0280E+00 4.3821E+00 -6.1615E+00 2.2758E+00 145 -6.0100E+00 -4.0350E+00 -1.7720E+00 1.8533E+00 -3.4578E+00 1.5776E+00 181 -7.6030E+00 -7.9500E-01 -6.0470E+00 4.2181E+00 -6.2552E-01 -1.5844E-02 185 -8.5010E+00 -2.3300E+00 -6.1790E+00 -7.0193E-01 1.5605E+00 -1.0806E+00 187 -3.6970E+00 -7.7220E+00 -2.4700E+00 -3.8794E+00 -3.1952E+00 6.3163E+00 189 -4.7470E+00 -9.9870E+00 -2.7590E+00 1.7072E+00 -1.3292E+01 -5.6002E+00 ---------------------------------------------------------------------------------------------------------------------------------- step eng_tot temp_tot eng_cfg eng_src eng_cou eng_bnd eng_ang eng_dih eng_tet time(ps) eng_pv temp_rot vir_cfg vir_src vir_cou vir_bnd vir_ang vir_con vir_tet cpu (s) volume temp_shl eng_shl vir_shl alpha beta gamma vir_pmf press ---------------------------------------------------------------------------------------------------------------------------------- 0 1.2483E+08 3.0000E+02 1.2483E+08 2.5787E+06 0.0000E+00 1.2225E+08 6.1460E+00 7.8775E+02 0.0000E+00 0.00000 1.1556E+07 0.0000E+00 3.3981E+08 -3.1072E+07 0.0000E+00 3.7088E+08 0.0000E+00 0.0000E+00 0.0000E+00 0.1 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -6.8752E+04 ---------------------------------------------------------------------------------------------------------------------------------- time elapsed since job start: 0.063 sec ---------------------------------------------------------------------------------------------------------------------------------- step eng_tot temp_tot eng_cfg eng_src eng_cou eng_bnd eng_ang eng_dih eng_tet time(ps) eng_pv temp_rot vir_cfg vir_src vir_cou vir_bnd vir_ang vir_con vir_tet cpu (s) volume temp_shl eng_shl vir_shl alpha beta gamma vir_pmf press ---------------------------------------------------------------------------------------------------------------------------------- 1 1.2628E+08 5.8520E+05 1.2483E+08 2.5787E+06 0.0000E+00 1.2225E+08 6.1460E+00 7.8775E+02 0.0000E+00 0.00010 1.3976E+07 0.0000E+00 3.3981E+08 -3.1072E+07 0.0000E+00 3.7088E+08 0.0000E+00 0.0000E+00 0.0000E+00 0.1 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -6.8165E+04 rolling 1.2628E+08 5.8520E+05 1.2483E+08 2.5787E+06 0.0000E+00 1.2225E+08 6.1460E+00 7.8775E+02 0.0000E+00 averages 1.3976E+07 0.0000E+00 3.3981E+08 -3.1072E+07 0.0000E+00 3.7088E+08 0.0000E+00 0.0000E+00 0.0000E+00 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -6.8165E+04 ---------------------------------------------------------------------------------------------------------------------------------- 50 1.2434E+08 1.5181E+07 8.6666E+07 2.4960E+05 0.0000E+00 8.6416E+07 7.6470E+00 7.7596E+02 0.0000E+00 0.00500 5.6513E+07 0.0000E+00 2.7884E+08 -3.0316E+06 0.0000E+00 2.8188E+08 0.0000E+00 0.0000E+00 0.0000E+00 0.1 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -4.1171E+04 rolling 1.2467E+08 3.0763E+07 4.8317E+07 6.5331E+05 0.0000E+00 4.7662E+07 1.0349E+01 7.4649E+02 0.0000E+00 averages 1.2292E+08 0.0000E+00 1.5795E+08 -7.8918E+06 0.0000E+00 1.6584E+08 0.0000E+00 0.0000E+00 0.0000E+00 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -1.0626E+03 ---------------------------------------------------------------------------------------------------------------------------------- 100 1.1977E+08 2.5558E+07 5.6340E+07 2.4380E+05 0.0000E+00 5.6096E+07 1.0932E+01 7.8518E+02 0.0000E+00 0.01000 8.7243E+07 0.0000E+00 2.2445E+08 -2.9529E+06 0.0000E+00 2.2740E+08 0.0000E+00 0.0000E+00 0.0000E+00 0.2 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 -1.9744E+04 rolling 1.2318E+08 3.2070E+07 4.3587E+07 4.5891E+05 0.0000E+00 4.3127E+07 9.5630E+00 7.4649E+02 0.0000E+00 averages 1.2321E+08 0.0000E+00 1.5909E+08 -5.5496E+06 0.0000E+00 1.6464E+08 0.0000E+00 0.0000E+00 0.0000E+00 2.7000E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 1.9383E+01 ---------------------------------------------------------------------------------------------------------------------------------- DL_POLY_3 terminated due to error 445 |
67楼2010-04-01 10:24:23
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对test13,就像你所说的周期性边界条件的影响.在vmd上那样显示是因为在dl_poly中的history上考虑周期性边界条件的,所以在VMD显示的时候,就有的靠近边界的分子的键就是断开的或者拉长的...所以我觉得test13 没有什么问题, 生成的history文件不影响分析,只是显示不好,这个问题我是这样理解的..... 而我的自己的体系,进行的是一个nvt berendesen 0.1 设置的模拟,就是跑不起来老是出错...我觉得要么是体系太不平衡,要么是我的CONFIG的设置不合理... 不知道你们都是怎么处理一个体系,比如说前期要不要进行一个 minimize. 还有就是在跑md的时候要不要加一段时间的equilibrium..... |
69楼2010-04-01 16:12:35
75楼2010-04-08 09:53:40
77楼2010-04-08 15:04:23
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您好,又来麻烦了.. 因为HISTORY的坐标不能直接用来统计分析(从前面的几个截图可以看出来,有的分子是断开的). 所以需要一定的转换吧,下面这段程序是在官方论坛上面有人这样写的,虽然讲的很清楚,可是我不明白他的算法是什么意思? 大家能给解释一下吗?谢谢!! here is a way to generate image flags (or unwrapped coordinates) from the HISTORY file which contains the wrapped coordinates: Assumptions: 1. All the atoms listed in the first configuration listed in the HISTORY file are assumed to be inside the box 2. The time between successive configurations in the HISTORY file is small enough for the atoms to not cross the simulation box boundaries more than once 3. Simulation box is cuboid, should be easily modifiable for other geometries Procedure: 1. Initialize the image flags ix, iy and iz in the x, y and z directions to 0, i.e. Code:ix = 0; iy = 0; iz = 0; where i = index of atoms going from 1 to nAtoms 2. Read the coordinates of all the atoms in the first configuration (config_old) and label them x_old, y_old and z_old 3. Read the coordinates of all the atoms from the next configuration (config_new) and label them x_new, y_new and z_new 4. The image flags for the configuration denoted as 'config_new' are then given as follows Code: ix = ix+int(2*(x_old-x_new)/L_x); iy = iy+int(2*(y_old-y_new)/L_y); iz = iz+int(2*(z_old-z_new)/L_z); where, int(k) = the integer part of the floating point number k L_x = Simulation box length in the x direction L_y = Simulation box length in the y direction L_z = Simulation box length in the z direction Note 1. If the box were cubic, L_x = L_y = L_z = L 2. Do not reset the image flags to zero, just keep on incrementing them 5. The unwrapped coordinated for the configuration denoted as 'config_new' are then given as Code: x_uw = x_new+L_x*ix y_uw = y_new+L_y*iy z_uw = z_new+L_z*iz 6. You can then use the unwrapped coordinates to fine the diffusion, etc. |
78楼2010-04-08 15:17:20
81楼2010-04-17 12:35:20
84楼2010-04-18 13:36:02
88楼2010-05-04 22:06:06