求助：想复刻文献跟着学gromacs,对聚合物优化这段代码不会敲

fenghua

"The MD simulation of the interaction between the polystyrene and tetracycline was conducted using the GROMACS package (version2018.4) : the GROMOS54a7 force field was used for the polystyrene and tetracycline , while the SPC/E model was used to simulate water molecules . The polystyrene was represented as a polymer, which was constructed according to procedures similar to those described in Tan et al. (2020): first, polymer chains each containing 20 polystyrene monomers were optimized with the B3LYP functional and 6–311G(d,p) basis sets . These were then utilized to generate 30-chain polystyrene polymers for the MD simulation. As the simulation results showed (Fig. S1), the polystyrene polymers reached equilibrium after 50 ns under a constant pressure of 1 bar and temperature rising   from 0 to 300 K at a constant rate of 0.01 K⋅ps−1."这个是文献的原文，主要是最后一段的参数不会设置     

Seyilaxa

最后一段的参数指的是哪一步的参数，如果优化指B3LYP/6-311G(d,p)做Optimization，那是量化计算的范畴，用gaussian或者ORCA算，输入文件可以用Multiwfn生成；如果指最后升温的那步，在.mdp文件中设置annealing相关的选项控制升温速率https://manual.gromacs.org/curre ... simulated-annealing

fenghua

Seyilaxa 发表于 2024-5-25 17:23
最后一段的参数指的是哪一步的参数，如果优化指B3LYP/6-311G(d,p)做Optimization，那是量化计算的范畴，用g ...

嗯，谢谢老师，所指的就是升温最后那一步

sobereva

参考北京科音分子动力学与GROMACS培训班（http://www.keinsci.com/workshop/KGMX_content.html）里的例子