使用gmxMMPBSA进行计算时轨迹文件的帧数是否会影响计算结果？

12313 · 发表于 Post on 2024-7-2 10:30:26

各位老师好，目前我正在使用gmxMMPBSA进行计算，我的轨迹文件的帧数是5001帧，并且在我的mmpbsa.in文件中startframe和endframe分别设置为1和5001，但是在进行计算时总是计算到某一帧就报错（如下图），所以我想是不是我的轨迹文件的帧数太大了，但是又不知道如果大幅度减小自己轨迹文件的帧数，是否会对我的gmxMMPBSA的计算结果产生影响，想问一下各位老师

student0618 · 发表于 Post on 2024-7-2 11:00:08

本帖最后由 student0618 于 2024-7-2 11:08 编辑

Usually we need more than 100 frames to do MMPBSA, and the sampling interval should be longer than the autocorrelation time of the system.

Refer to the discussion in this thread on how to choose the frames for MMPBSA, which part of trajectory to use http://bbs.keinsci.com/forum.php ... 42&highlight=MMPBSA

For what happened exactly that caused the error you have, its better to check the other output files from the software, instead of just guessing.

12313 · 发表于 Post on 2024-7-2 12:03:26

student0618 发表于 2024-7-2 11:00
Usually we need more than 100 frames to do MMPBSA, and the sampling interval should be longer than t ...

Thanks for your answer.By the way,What is the sampling interval and the autocorrelation time of the system?
Are these two parameters in certain files? e.g. mmpbsa.in

student0618 · 发表于 Post on 2024-7-2 12:26:24

Sampling interval is how frequently a frame is selected from trajectory for calculation.
You can change the interval in mmpbsa.in (screenshot of input file taken from gmx_MMPBSA website )

Autocorrelation time depends on system. See https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/api/?h=autoc on more details on why we want to use an uncorrelated dataset. original publication of mmpbsa.py (https://doi.org/10.1021/ct300418h) also discusses on it.

低调的板凳 · 发表于 Post on 2024-7-2 14:38:24

5000帧的话在想要计算的平衡段平均取个200-300帧进行PB计算就行。假设500帧之后RMSD相对平衡，那就500-5000帧间隔20帧取一帧计算就行。

12313 · 发表于 Post on 2024-7-2 15:11:47

低调的板凳发表于 2024-7-2 14:38
5000帧的话在想要计算的平衡段平均取个200-300帧进行PB计算就行。假设500帧之后RMSD相对平衡，那就500-5000 ...

感谢老师的回复

12313 · 发表于 Post on 2024-7-2 15:42:10

低调的板凳发表于 2024-7-2 14:38
5000帧的话在想要计算的平衡段平均取个200-300帧进行PB计算就行。假设500帧之后RMSD相对平衡，那就500-5000 ...

老师，如果是要设置间隔20帧取一帧，是不是调整interval 这个参数啊？

12313 · 发表于 Post on 2024-7-2 16:21:27

student0618 发表于 2024-7-2 12:26
Sampling interval is how frequently a frame is selected from trajectory for calculation.
You can c ...

Thank you very much

低调的板凳 · 发表于 Post on 2024-7-3 10:46:16

12313 发表于 2024-7-2 15:42
老师，如果是要设置间隔20帧取一帧，是不是调整interval 这个参数啊？

可以直接在pb的脚本里调interval，也可以先用gmx trjconv把这些帧提出来，再计算pb。

12313 · 发表于 Post on 2024-7-3 11:36:00

低调的板凳发表于 2024-7-3 10:46
可以直接在pb的脚本里调interval，也可以先用gmx trjconv把这些帧提出来，再计算pb。

好的，谢谢老师

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[GROMACS] 使用gmxMMPBSA进行计算时轨迹文件的帧数是否会影响计算结果？