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本帖最后由 Rororozoroni 于 2023-12-18 10:10 编辑
我在使用官方所给minim.mdp文件对我建立的模型进行能量最小化（设置要跑5000step），但是跑了50多个step就报了以下的提示：
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (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.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
我注意到可以在mdp文件设置constraints=none，然后我将这一句写入minim.mdp文件，运行后仍然报了以上的提示，后续进行nvt就不跑了，跑到step0就说One or more water molecules can not be settled.Check for bad contacts and/or reduce the timestep if appropriate.Wrote pdb files with previous and current coordinates，我用vmd观察我的模型没有发现原子堆叠，相互之间是分开的没有重合或交叉，目前来看可能就是能量最小化没有运行成功，没有让体系能量最小化，所以跑不了nvt，请问遇到这种情况应该如何解决？
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发表于 Post on 2023-12-18 10:07:44
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楼主 Author
发表于 Post on 2023-12-18 16:37:39