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求助一下载体分子+药物分子MD失败的原因

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帖子模式

milk_q

发布时间: 2025-9-17 10:24

正文摘要:

载体分子10个（原子数目743），药物分子（小分子）4个，模拟盒12*12*12，使用10000步steep能量最小化，NVT平衡+NPT生产模拟，以下是我的mdp文件，大家可以看一下有什么问题吗 em_sd: define = -DFLEXIBLEintegrato ...

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milk_q 发表于 Post on 2025-9-17 15:00:04

student0618 发表于 2025-9-17 11:03
Use NPT equilibration first with Berendsen or c-rescale barostat to relax box size and density.

F ...

only water

student0618 发表于 Post on 2025-9-17 11:03:52

Use NPT equilibration first with Berendsen or c-rescale barostat to relax box size and density.

For long polymer like this you maybe need higher pressure to compress the box to desired density first before using the target density.

It may also be useful to use simulated annealing to relax initial configurations.

Btw, just wondering, is there any water or other solvent in this system?

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