Bug summary Hi, I am trying to calculate the mmpbsa between a protein and peptide. I used gromacs2023.02 and the pbc was removed from the trajectory. But since the version of gmx_MMPBSA is compatible with Gromacs2020, md_2020.tpr was reg...
gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files. It works with all GROMACS versions along with AmberTools >= 20. Please see the documentationhere Cite us
跑完MD后，用Home - gmx_MMPBSA Documentation (valdes-tresanco-ms.github.io)计算膜蛋白与配体的...
https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/517 先按照官方的env构建环境,但是你需要...
运行 gmx_MMPBSA -i mmpbsa_pb.in -cs md1.tpr -ct traj_centered.xtc -ci index.ndx -cg 4...
gmx_MMPBSA --create gb pb decomp 该文件列出了GB、PB方法做结合自由能计算和能量分解的所有参数,具体含义请见官方网站【9】。大部分情况下默认参数就够用了,只有少量需要修改。这里给一个精简版的mmpbsa.in文件: # General namelist varia...
gmx_MMPBSAprovides all theMMPBSA.pyfunctionalities to GROMACS users. In addition, other functionalities have been implemented that ease a number of calculations (e.g.MM/PB(GB)SA with user-defined internal dielectric constant, interaction entropy and C2 entropy calculations). A GUI applicationgmx_MM...
采用官网给的方法https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/installation/，先安装了Python...
前面我们介绍了李继存老师开发的用于计算GROMACS模拟轨迹中MMPBSA的脚本——gmx_mmpbsa.sh。有趣的是,还有一款同名工具gmx_MMPBSA,其功能更为强大。它搭建了GROMACS与AMBER分析模块之间的桥梁,支持用户计算MMPBSA和MMGBSA。就我个人而言,我更喜欢使用MMGBSA,因为它不仅计算速度更快,而且出现异常值的概率也比MMPBSA更低...
gmx_MMPBSA is rapidly becoming one of the main programs to perform end-point free energy calculations out there (~29k downloads so far). We are currently focused on optimizing the program, supporting new types of calculations, force fields, etc. However, the video tutorials are not that ...