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最近在尝试离子在水球中的溶剂化能,首先参考NAMD网站上的例子“Ubiquitin in a Water Sphere: Simulation with Non-Periodic Boundary Conditions”实现泛素在水球中的平衡后,尝试将其中最后一个水分子设为解耦分子,使用FEP法计算水分子在示例体系中的溶剂化能,结果在backward.fepout文件中出现dG=999999.999,在网上看到
- Different reasons why immediately after solvation (in the first step), the energy is VERY large (i.e. 999999):
- The protein or the solvent crosses the bounadry. For example, if a spherical boundary condition is specified and the protein is longer than the diameter of the sphere.
有可能是边界条件设置的问题(但是我用的是示例的参数),相关的参数如下所示,想请各位老师看一下问题出在哪里?还想请教一下MSMxmin、MSMxmax的选取有什么参考标准吗?
# Electrostatic Force Evaluation
MSM on
MSMGridSpacing 2.5
MSMxmin -5.0
MSMxmax 60.0
MSMymin -5.0
MSMymax 60.0
MSMzmin -15.0
MSMzmax 46
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423
sphericalBCr1 26.0
sphericalBCk1 10
sphericalBCexp1 2
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