gromacs学习及使用(4)——(待完善)

gromacs Fatal error: atom C2 not found in buiding block 79MET while combining tdb and rtp

1. gromacs力场选择
2. 如何选择合适的力场和水溶液模型
3. GROMACS蛋白配体分子动力学模拟结果分析简要笔记
4. GROMACS教程【02】分子动力学模拟结果分析常用命令（二）
5. 在使用pgb2gmx生成适配体的gro文件时，提示找不到N原子
6. GROMACS 遇到错误及解决方案
7. pdb2gmx 命令使用注意事项
8. 关于charmm36-jul2022.ff报错的问题（Fatal error:atom C1 not found in buid
9. gromacs pdb2max
10. Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
11. 教你合理选择力场-分子动力学

freeze group

freeze group
Atoms that belong to a freeze group are kept stationary in the dynamics.
属于冻结组的原子在动力学中保持静止。
This is useful during equilibration, e.g. to avoid badly placed solvent molecules giving unreasonable kicks to protein atoms,
这在平衡期间是有用的（例如避免放置不良的溶剂分子对蛋白质原子产生不合理的踢击，
although the same effect can also be obtained by putting a restraining potential on the atoms that must be protected.
尽管通过对必须被保护的原子施加抑制电势也可以获得相同的效果。
The freeze option can be used, if desired, on just one or two coordinates of an atom, thereby freezing the atoms in a plane or on a line.
如果需要，冻结选项可以仅在原子的一个或两个坐标上使用，从而将原子冻结在平面或直线上。
When an atom is partially frozen, constraints will still be able to move it, even in a frozen direction.
当原子被部分冻结时，约束仍然能够移动它，即使是在冻结的方向上。
A fully frozen atom can not be moved by constraints.
完全冻结的原子不能被约束移动。
Many freeze groups can be defined.
可以定义许多冻结组。
Frozen coordinates are unaffected by pressure scaling; in some cases this can produce unwanted results, particularly when constraints are also used (in this case you will get very large pressures).
冻结坐标不受压力缩放的影响；在某些情况下，这可能会产生不想要的结果，特别是当还使用约束时（在这种情况下，您将获得非常大的压力）。
Accordingly, it is recommended to avoid combining freeze groups with constraints and pressure coupling.
因此，建议避免将冻结组与约束和压力耦合相结合。
For the sake of equilibration it could suffice to start with freezing in a constant volume simulation, and afterward use position restraints in conjunction with constant pressure.
为了平衡，在恒定体积模拟中从冻结开始，然后结合恒定压力使用位置约束就足够了。