如何在非MS中实现模拟盒子的original显示而非in cell

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想模仿文献进行聚合物的拉伸模拟（[size=8.00013px]https://doi.org/10.1002/anie.202115904 ）。因本人为新手小白，选用方法为在material studio中建模然后导出data至lammps弛豫拉伸。周期性盒子in cell模型老板觉得太丑，如何实现文献这种效果呢？该组使用相同模拟方法同年还发了一篇[size=8.00013px]https://doi.org/10.1021/jacs.1c10278

文献的模拟部分描述如下：Atomistic molecular dynamics simulations were performed to elucidate effect of the chain deformation on evolution of the hydrogen bonds. The General Amber Force Field (GAFF) was used to model the isosorbide/isomannide-containing polyurethanes. The forces on the atoms were calculated by differentiating the potential energy of the system, which consisted of bonded (bonds, angle, dihedral, and improper potentials) interactions as well as nonbonded interactions (van de Waals and electrostatic).
In GAFF, the van de Waals interactions are represented by the Lennard-Jones (LJ) potentials with parameters given for each homogeneous atomic pair (𝑟𝑖𝑖 and 𝜖𝑖𝑖), while the parameters for heterogeneous pairs are determined as 𝑟𝑖𝑗 = 𝑟𝑖 + 𝑟𝑗 and 𝜖𝑖𝑗 = √𝜖𝑖𝜖𝑗. The LJ potential is truncated at a cutoff distance of 10 A. The weighting coefficient for the 1-4 interaction was set to 0.5 for the LJ-interactions and 0.833 for the Columbic interactions. Partial charge distributions were obtained from DFT calculations using B3LYP 6-31G* (d,p) basis set for AM1 optimized structures. These simulations were performed using Gaussian 09. Note that the partial charges are averaged for atoms with the same chemical environment for simplicity. The interaction parameters for non-bonded/bonded interactions are summarized in Table S3.
The information about macromolecular structure (list of bonds, angles, dihedrals, improper dihedrals) was generated by Topotools plugins in VMD. Each polymer chain had 16 repeating units. The two ends of each polymer chain were connected across the periodic boundary along x direction forming a loop representing an infinitely long polymer chain. There were two identical chains in the periodic simulation box with equilibrium dimensions Lx=80 Å and Ly=Lz=40 Å. These polymer chains adopted a bundle-like conformation. The system was equilibrated for 5000 ns. After completion of the equilibration step the simulation box was deformed along x direction with a constant strain rate of 2.5*10-6 fs-1. During the deformation process, the atom velocities in y and z directions were coupled to the thermostat to maintain system temperature. All simulations were performed using the following setup: PPPM method for calculations of the electrostatic interactions with targeted accuracy 10-4, vacuum dielectric constant ε = 1.0, T = 293K, Langevin thermostat (damping parameter 10 fs), and time step t = 0.5 fs. All simulations were performed using LAMMPS with GPU acceleration.

含光君

MS里边dispaly style里面改成original把边框去了，底色换成白的就行；或者直接用vmd看。

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含光君 发表于 2022-10-21 13:52
MS里边dispaly style里面改成original把边框去了，底色换成白的就行；或者直接用vmd看。

您好，因为我拉伸是在lammps中做的，这个怎么再用MS打开呢？VMD直接打开的话是in cell的，请问该如何调整显示方式呢

含光君

VMD里面选取相应帧导出为pdb文件，然后用MS打开。但是VMD可视化功能比MS强很多啊，没必要用MS看这么大的分子。

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含光君 发表于 2022-10-22 23:37
VMD里面选取相应帧导出为pdb文件，然后用MS打开。但是VMD可视化功能比MS强很多啊，没必要用MS看这么大的分 ...

非常感谢您！再请问一下可以直接在VMD中显示成一样的效果吗？

含光君

当然可以，稍微摸索一下就可以搞定。