标题: 使用非周期性边界条件计算溶剂化能时出现dG=99999.9 [打印本页] 作者Author: s99r 时间: 2022-6-9 19:25 标题: 使用非周期性边界条件计算溶剂化能时出现dG=99999.9 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.