starting structure for MD run

moiumuio · 发表于 Post on 2025-10-14 13:26:20

Hi everyone,
I am just starting to learn Molecular Dynamics. My task is to run an MD job of a polymer chain to simulate the self-healing property. I would like to know if the starting polymer for the structure construction needs to be optimised first?
Thank you for your answer

moiumuio · 发表于 Post on 2025-10-16 16:30:00

牧生发表于 2025-10-14 21:54
Well, I strongly recommend you to use this tool:

http://bbs.keinsci.com/thread-55201-1-1.html

Thank you so much
That post is very valuable.

sobereva · 发表于 Post on 2025-10-15 21:08:44

If there is no close contact between any atoms in your initial structure, then optimization (minimization) is not absolutely needed before MD.

牧生 · 发表于 Post on 2025-10-14 21:54:30

本帖最后由牧生于 2025-10-14 21:58 编辑

Well, I strongly recommend you to use this tool:

http://bbs.keinsci.com/thread-55201-1-1.html

The polymer you establish through this tool is reasonable, so there is no need to optimize the polymer again.

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[GROMACS] starting structure for MD run

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