计算化学公社

标题: 蛋白质ATP体系模拟崩溃求助 [打印本页]

作者
Author: xiaoai 时间: 2024-5-23 11:31
标题: 蛋白质ATP体系模拟崩溃求助
本帖最后由 xiaoai 于 2024-5-23 11:34 编辑

蛋白质ATP体系模拟限制性动力学模拟崩溃，已按照http://sobereva.com/soft/Sobtop/#FAQ8  没有找到明显问题。grompp有几个警告  麻烦各位老师看看是否为严重警告
WARNING 1 [file pr.mdp]:
  The Berendsen barostat does not generate any strictly correct ensemble,
  and should not be used for new production simulations (in our opinion).
  For isotropic scaling we would recommend the C-rescale barostat that also
  ensures fast relaxation without oscillations, and for anisotropic scaling
  you likely want to use the Parrinello-Rahman barostat.

NOTE 1 [file topol.top, line 55]:
  System has non-zero total charge: -0.000500
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

WARNING 2 [file topol.top, line 55]:
  You are using Ewald electrostatics in a system with net charge. This can
  lead to severe artifacts, such as ions moving into regions with low
  dielectric, due to the uniform background charge. We suggest to
  neutralize your system with counter ions, possibly in combination with a
  physiological salt concentration.

NOTE 2 [file pr.mdp]:
  Removing center of mass motion in the presence of position restraints
  might cause artifacts. When you are using position restraints to
  equilibrate a macro-molecule, the artifacts are usually negligible.

在能量极小化步骤结果会出现
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 50 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

目前做了两次最小化还是存在这个问题，更改参数退火以及更换方法都尝试了
能量极小化结果为
Steepest Descents converged to machine precision in 329 steps,
but did not reach the requested Fmax < 50.
Potential Energy  = -1.9281260e+06
Maximum force    =  9.3773456e+02 on atom 5795
Norm of force    =  7.4086277e+00

这里附上其他文件请各位老师指点崩溃原因可能所在
我之前尝试一个蛋白质和ATP体系在限制性动力减小步长后正常运行
这次为四个蛋白质的复合体和ATP  不知道是不是体系过大需要注意哪里  请各位老师指点

作者
Author: sobereva 时间: 2024-5-23 15:16
那些warning、note都可以无视
http://sobereva.com/soft/Sobtop/#FAQ8里该说的都说了，包括去掉某些1-4项的事

作者
Author: xiaoai 时间: 2024-5-23 20:43

sobereva 发表于 2024-5-23 15:16
那些warning、note都可以无视
http://sobereva.com/soft/Sobtop/#FAQ8里该说的都说了，包括去掉某些1-4项 ...

感谢老师。修改了pairs现在已经可以正常模拟了。老师我想再具体问一下，我现在是吧pairs里面所有O-H的删掉。不知道这样操作是不是准确，还是应该找到异常的O-H，然后删掉。因为我用vmd cartoon看轨迹不知道如何观察是哪个O和H异常，请问老师这个是否有相关博文学习

作者
Author: sobereva 时间: 2024-5-24 04:28

xiaoai 发表于 2024-5-23 20:43
感谢老师。修改了pairs现在已经可以正常模拟了。老师我想再具体问一下，我现在是吧pairs里面所有O-H的删 ...

只删异常的
甭用new cartoon不就完了，用CPK、licorice、line之类的能显示所有原子的

欢迎光临计算化学公社 (http://bbs.keinsci.com/)