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gromacs运行问题已有2人参与
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各位大神，我用一个小程序对膜进行剪切处理后，进行能量最小化时出现下列问题： Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 500000 Step Time Lambda 0 0.00000 0.00000 DD step 0 load imb.: force 12.9% Step Time Lambda 1 1.00000 0.00000 Step Time Lambda 2 2.00000 0.00000 Step Time Lambda 3 3.00000 0.00000 Step Time Lambda 4 4.00000 0.00000 Step Time Lambda 5 5.00000 0.00000 Step Time Lambda 6 6.00000 0.00000 Step Time Lambda 7 7.00000 0.00000 Step Time Lambda 8 8.00000 0.00000 Step Time Lambda 9 9.00000 0.00000 Step Time Lambda 10 10.00000 0.00000 Step Time Lambda 11 11.00000 0.00000 Step Time Lambda 12 12.00000 0.00000 Step Time Lambda 13 13.00000 0.00000 Step Time Lambda 14 14.00000 0.00000 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = 1.5981487e+19 Maximum force = inf on atom 5867 Norm of force = inf 这是嘛回事呢，咋解决？ |
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softmatter
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2楼2014-04-12 15:35:51
3楼2014-04-12 23:16:02
softmatter
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4楼2014-04-12 23:51:27
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fegg7502: 金币+1, 鼓励交流 2014-05-05 08:22:47
fegg7502: 金币+1, 鼓励交流 2014-05-05 08:22:47
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Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.661 nm, LJ-14, atoms 4431 4452 multi-body bonded interactions: 0.661 nm, Proper Dih., atoms 4431 4452 Minimum cell size due to bonded interactions: 0.727 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.771 nm Estimated maximum distance required for P-LINCS: 0.771 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 0.964 nm The maximum allowed number of cells is: X 11 Y 11 Z 6 Domain decomposition grid 8 x 1 x 1, separate PME nodes 0 PME domain decomposition: 8 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Will do PME sum in reciprocal space. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2 Long Range LJ corr.: <C6> 6.3119e-03 System total charge: -0.000 Generated table with 1100 data points for Ewald. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ12. Tabscale = 500 points/nm Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing x86_64 SSE2 support... present. Removing pbc first time Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 18564 There are inter charge-group constraints, will communicate selected coordinates each lincs iteration Linking all bonded interactions to atoms There are 45500 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 The initial domain decomposition cell size is: X 1.44 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.200 nm multi-body bonded interactions (-rdd) 1.200 nm atoms separated by up to 5 constraints (-rcon) 1.438 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 2 The minimum size for domain decomposition cells is 1.049 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.73 The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 1.200 nm multi-body bonded interactions (-rdd) 1.049 nm atoms separated by up to 5 constraints (-rcon) 1.049 nm Making 1D domain decomposition grid 8 x 1 x 1, home cell index 0 0 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: POPC There are: 18928 Atoms Charge group distribution at step 0: 1547 1628 1762 1544 1654 1623 1699 1647 Grid: 4 x 13 x 7 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 1.41e-06 Initial temperature: 0.00294003 K Started mdrun on node 0 Sat Apr 12 23:30:51 2014 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 1.79277e+04 2.19389e+04 1.21721e+03 7.28810e+02 3.52807e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential -7.88621e+04 -3.55517e+03 -7.88547e+04 -3.15743e+05 -3.99921e+05 Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) 5.89721e+00 -3.99915e+05 3.71179e-02 -1.53150e+02 -5.35095e+02 Constr. rmsd 我也不清楚那里有问题，然后命令停止，输出几个被切割开的pdb文件，这是神马节奏？ |
5楼2014-04-13 00:16:30
softmatter
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youngfi
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