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longwei1221铁虫 (小有名气)
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[求助]
forcite做动力学计算出错了，哪位帮忙看一下是什么原因
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我想计算水的自扩散系数，用几种方法都出错了。下面是其中一种使用forcite来计算的结果，哪位看看什么参数设置错误导致中断的？ 我分两种方法建模，一个是用AC模块设置密度为1，另外一种是直接建模用forcite的几何优化来建模再做动力学模拟。同时在计算动力学我也尝试了discovery和forcite，结果都中断失败了，不知道什么原因，哪位帮忙看一下吧，谢谢啦！ 下面分别是forcite和discovery的错误提示。另外如果谁知道计算扩散系数方法，麻烦告知一声，不胜感激，我愿意奉送全部的金币 Forcite ------- Task : Dynamics Version : 5.0 Build date : Oct 22 2009 Host : meilongwei-PC Threads : Parallel 3 Operating system : Windows Task started : Tue Oct 23 16:48:46 2012 ---- Dynamics parameters ---- Ensemble : NPT Temperature : 293.00 K Control method : Velocity Scale Temp. difference : 10.00 K Pressure : 0.00010 GPa Control method : Andersen Cell time constant : 1.0000000 ps Timestep : 10.00 fs Number of steps : 1000000 Duration : 10000 ps Initial velocities : Random Random number seed : 1350982127 ---- Energy parameters ---- Forcefield : Universal Electrostatic terms: Summation method : Atom based Truncation method : Cubic spline Cutoff distance : 15.5 A Spline width : 1 A Buffer width : 0.5 A van der Waals terms: Summation method : Atom based Truncation method : Cubic spline Cutoff distance : 15.5 A Spline width : 1 A Buffer width : 0.5 A Dynamics calculation - Aborting dynamics. An unphysical integration step (>100 Angstroms) has been detected. Try reducing the time step or relaxing the structure first. discovery错误提示 DISCOVER Molecular Simulation Program Version: 2009.1 Build: Oct 22 2009 Date: Tue Oct 23 15:49:33 2012 User Name: MEILONGWEI-PC$ Host Name: meilongwei-PC Host Type: Windows Threads: 1 --------------------------------------------------------------- Checked out license feature: MS_discover_MP --------------------------------------------------------------- randomSeed is set to 978573 Line 7:BTCL> autoEcho off --------------------------------------------------------------- Checked out license feature: MS_compass_MP --------------------------------------------------------------- INPUT FILES ___________ File Type Name --------- ---- Forcefield C:\PROGRA~1\Accelrys\MATERI~1.0\etc\Gateway\..\..\share\Discover\res/compass.frc Molecular data Molecule1.mdf Coordinate Molecule1.car Periodic Boundary Conditions ____________________________ Length (A) Angle (degrees) ---------- --------------- a 10.61650 alpha 90.00000 b 10.61650 beta 90.00000 c 10.61650 gamma 90.00000 MOLECULAR TOPOLOGY __________________ Number of molecules: 40 Number of residues: 40 Number of atoms: 120 (asymmetric unit: 120) Number of atom types: 3 Number of bonds: 80 Number of consolidated angles: 40 FORCEFIELD OPTIONS __________________ Filename : compass.frc Definition name : cff91 Version : 2.8 Last modification date : 3/6/2007 # of automatic parameters : 0 NONBOND ENERGY CUTOFFS ______________________ Cutoff (A) Spline Width (A) Buffer Width (A) vdW 9.50 1.00 0.50 Coulomb -- -- -- NONBOND ENERGY EWALD PARAMETERS _______________________________ Accuracy (kcal/mol) Update Width (A) vdW -- -- Coulomb 0.01000000 1.00 Summation method for vdW : Atom based Summation method for Coulomb : Ewald Dielectric : 1.00 NOTE: Pressure and energy tail corrections will be added to all subsequent energy evaluations MOLECULAR DYNAMICS __________________ Ensemble : NPT Temperature : 293.00 K Control Method : Andersen, Collision frequency is every 68 steps Pressure : 0.0001 GPa Stress : Sxx = 0.0000 GPa Syy = 0.0000 GPa Szz = 0.0000 GPa : Syz = 0.0000 GPa Sxz = 0.0000 GPa Sxy = 0.0000 GPa Control Method : Berendsen , tau = 0.1443 psec , compressibility = 0.5000 Timestep : 1.00 fs Duration :1000000.00 fs Integration Method : Velocity Verlet Initial Velocities : Random Velocities from Boltzmann distribution Initial Temp. : 293.00 K Error: Dynamics: Energy difference between successive steps in dynamics is greater than the user defined variable DEVIATION, 5000.000 invoked from within "dynamics \ time = 1000000.00 \ timestep = 1.00 \ initial_temperature = 293.00 \ ensemble = NPT \ temperature_control_method = ande ..." Total time used by DISCOVER: 24 mins 7.05 secs (1447.05 secs) Completion date: Tue Oct 23 16:13:41 2012 Exiting Discover: An ERROR has occurred! |
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wangzhikun
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5楼2012-10-24 16:25:00
wangzhikun
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2楼2012-10-23 19:54:35
longwei1221
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麻烦帮忙看一下这个错误是什么原因导致的好吗？被告知能量太大，不知道该如何设置可以减小这个能量 Forcite ------- Task : Dynamics Version : 5.0 Build date : Oct 22 2009 Host : meilongwei-PC Threads : Parallel 3 Operating system : Windows Task started : Wed Oct 24 10:17:10 2012 ---- Dynamics parameters ---- Ensemble : NPT Temperature : 300.00 K Control method : Andersen Collision ratio : 1.0000000 Pressure : 0.00010 GPa Control method : Andersen Cell time constant : 1.0000000 ps Timestep : 1.00 fs Number of steps : 1000000 Duration : 1000 ps Initial velocities : Random Random number seed : 1351045030 ---- Energy parameters ---- Forcefield : Universal Electrostatic terms: Summation method : Atom based Truncation method : Cubic spline Cutoff distance : 18.5 A Spline width : 1 A Buffer width : 0.5 A van der Waals terms: Summation method : Atom based Truncation method : Cubic spline Cutoff distance : 18.5 A Spline width : 1 A Buffer width : 0.5 A ---- Thermostat ---- Andersen collision period: every 222 steps. Dynamics calculation - Deviation in total energy (2.21112e+012) between successive steps was greater than the specified maximum (5000). Task terminated : Wed Oct 24 10:17:17 2012 Total CPU time used by Forcite: 4 seconds (3.82s) Termination status : Error |
3楼2012-10-24 10:20:38
huangshuang1
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4楼2012-10-24 10:29:46