求助：混合膜的模拟中，能量最小化时提示错误信息Energy minimization has stopped.

yian · 发表于 Post on 2023-5-17 21:57:43

各位老师，我初学混合膜的模拟，组成混合膜的两种磷脂分子是在GROMOS54A8力场下的，步骤是跟着培训班教程一步一步走的，但是在能量极小化步骤中出现了以下报错信息：
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (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.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.

Polak-Ribiere Conjugate Gradients converged to machine precision in 100 steps,
but did not reach the requested Fmax < 100.
Potential Energy  =  4.2020992e+08
Maximum force    =  4.0882774e+08 on atom 3289
Norm of force    =  3.5014327e+06

不知道该怎么解决，请老师们指教，谢谢。
相关文件附上

memwat.rar (171.65 KB, 下载次数 Times of downloads: 7)

mixmem.rar (36.83 KB, 下载次数 Times of downloads: 5)

DPO.itp (10.93 KB, 下载次数 Times of downloads: 3)

POP.itp (10.43 KB, 下载次数 Times of downloads: 3)

topol.top (1.42 KB, 下载次数 Times of downloads: 12)

em.mdp (389 Bytes, 下载次数 Times of downloads: 5)

em.log (19.91 KB, 下载次数 Times of downloads: 1)

zdworld · 发表于 Post on 2023-5-18 00:13:19

这么大的力一定是拓扑出问题，建议检查结构，能量最小化如果有别的报错应该会输出错误帧的pdb文件。看一下是从哪个原子开始崩掉的。.top别把分子一个个列出来啊，直接写name写数量就好了。

sobereva · 发表于 Post on 2023-5-18 00:15:51

pdb文件里DLP残基是什么东西？都没有定义，和[molecules]里明显不符
必须严格确保pdb文件里原子顺序和[molecules]部分的对应关系

yian · 发表于 Post on 2023-5-19 16:16:56

谢谢老师我修改后能量极小化显示粒子间的距离有问题，再试了几次报错信息又是
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (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.
请问这会不会是我的初始结构有问题啊我初学混合膜模拟每一步都是按照教程来的可能细节不太懂请老师指教谢谢

		自动登录 Automatic login	找回密码 Forget password
密码 Password			注册 Register

[GROMACS] 求助：混合膜的模拟中，能量最小化时提示错误信息Energy minimization has stopped.