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mdrun时出错
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mdrun -s aa.tpr -o aa.trr -c aa.gro & 出现了如下的提示错误： step 11: Water molecule starting at atom 180665 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates step 13: Water molecule starting at atom 180665 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates 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. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 31 steps, but did not reach the requested Fmax < 1000. Potential Energy = -3.1653622e+06 Maximum force = 9.5183238e+05 on atom 180665 Norm of force = 2.3416899e+03 下面是我的em.mdp文件 em.mdp er spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /lib/cpp constraints = none define = -DFLEX_SPC ; Parameters describing what to do, when to stop and what to save integrator = steep dt = 0.002 emtol = 1000.0 emstep = 0.01 nsteps = 3000 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = pme rcoulomb = 1.0 rvdw = 1.0 fourierspacing =0.12 pme_order =4 optimize_fft =yes freezegrps =Protein UNK POP freezedim =Y Y Y Y Y Y Y Y Y 我也尝试了改变em.mdp文件中的一些参数(只对一个参数做了修改)： 1.em.mdp文件中的freezegrps改为Protein UNK能量能很好地收敛，下面是它的显示结果： Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 3000 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 1678 steps Potential Energy = -4.2245720e+06 Maximum force = 9.5952905e+02 on atom 9032 Norm of force = 1.1612597e+01 2.em.mdp文件中的emstep改为0.00001（参照别人的回答), 结果显示为： Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 3000 writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 32 steps Potential Energy = -3.0919205e+06 Maximum force = 9.1417908e+02 on atom 122811 Norm of force = 1.1197423e+02 这样的结果应该是有问题的吧，只跑了32步。 3.integrator改为md, 结果为： Writing final coordinates. Average load imbalance: 0.2 % Part of the total run time spent waiting due to load imbalance: 0.1 % Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 7515.940 7515.940 100.0 2h05:15 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 63.678 3.946 0.115 208.755 gcq#290: "Oh, There Goes Gravity" (Eminem) 请问一下，我应该怎么做才是合理的？谢谢！ |
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6楼2011-04-19 13:30:13
★ ★ ★ ★
小木虫(金币+0.5):给个红包，谢谢回帖
Jfreda(金币+5): 2011-04-18 19:08:54
zh1987hs(金币+3): 谢谢 2011-04-18 21:33:02
小木虫(金币+0.5):给个红包，谢谢回帖
Jfreda(金币+5): 2011-04-18 19:08:54
zh1987hs(金币+3): 谢谢 2011-04-18 21:33:02
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Steepest Descents converged to Fmax < 1000 in 32 steps Potential Energy = -3.0919205e+06 Maximum force = 9.1417908e+02 on atom 122811 Norm of force = 1.1197423e+02 这样的结果应该是有问题的吧，只跑了32步。 虽然只跑了32步，不过你的力已经基本收敛了，应该没有什么问题了。应该不用freegroup,如果要限制原子的话，可以尝试使用define. |
2楼2011-04-18 18:42:24
3楼2011-04-18 19:10:46
4楼2011-04-19 09:07:48
