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本帖最后由 光荣道彭于晏 于 2022-3-4 21:37 编辑
我尝试通过mdp中的deform参数模拟盒子在常温常压下的压缩/拉伸过程，但是对具体如何设置参数并不清楚。通过谷歌找到了有人在GROMACS论坛发的帖子，帖子里面应该是官方人员的回复。帖子内容如下：（Uniaxial deformation of polymer and stress calculation）
alevilla：If you want to deform in x axis, you can use the option “deform” in combination with pressure coupling semiisotropic in place of anisotropic and compressibility 0. in x and y direction.
D_C：2. If you want to perform uniaxial extension (or compression), you will only want deformation in the direction of strain, thus only the x component should be defined, and all others zero. I’d implore you to play around with changing a(x) … c(y) to see what they do to your system. Should only take a few minutes and will give you a strong understanding of what’s actually happening.
3. If you are performing uniaxial extension in the x-direction, then you should be looking into the Pxx component of your stress tensor. The stress in the x-direction, Sx, would be calculated as Sx=-Pxx, per Lyulin, et al. 11 It is worth noting there are other ways to calculate this.
4. If you consider what 1E-2 nm/ps would look like in a real world experiment, you’ll quickly realize that this is a ludicrous speed 6 value. Given many tensile tests are performed at cm/min, a more appropriate value may be ~1E-7 nm/ps. This would clearly require quite long simulation times.
根据以上内容，将参数设置为：Pcoupl= parrinello-rahman
pcoupltype = semiisotropic
tau_p = 2.0
ref_p = 1.01325 1.01325
compressibility = 0 4.5e-5
deform = -0.04 0 0 0 0 0
并进行100ps的模拟，发现盒子在x轴方向被压缩，同时y轴的宽度不变，z轴被“拉长”，如图1.
而对于单纯在x轴方向的压缩，上述这种设置方式显然是不符合要求的，y轴方向和z轴方向应该同时有变化，同时希望保持矩形盒子形状。根据帖子内容，将参数设置为：
Pcoupl = parrinello-rahman
pcoupltype = anisotropic
tau_p = 2.0
ref_p = 1.01325 1.01325 1.01325 1.01325 1.01325 1.01325
compressibility = 4.5e-5 0 0 0 0 0
deform = -0.04 0 0 0 0 0
但是，grompp会报错：“All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?”和“A box element has deform set and compressibility > 0”，无法生成tpr文件。
我的问题是，对于一个单纯的x轴压缩过程（常温常压），应该如何设置控压参数和deform参数？
谢谢各位老师！！
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发表于 Post on 2022-3-4 21:35:32
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