sobereva 发表于 2026-1-7 04:30
老生常谈的问题，仔细看下文RMSD部分
谈谈怎么判断分子动力学模拟是否达到了平衡
http://sobereva.com/62 ...

谢谢老师

student0618 发表于 2026-1-6 15:51
参考GROMACS手册 https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html

谢谢老师

老生常谈的问题，仔细看下文RMSD部分
谈谈怎么判断分子动力学模拟是否达到了平衡
http://sobereva.com/627（http://bbs.keinsci.com/thread-27122-1-1.html）

YuniJ 发表于 2026-1-6 14:30
我想请教一下原理是什么嘞？我对pbc进行了-center -pbc mol -ur compact和-fit rot+trans

参考GROMACS手册 https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html

cluster clusters all the atoms in the selected index such that they are all closest to the center of mass of the cluster, which is iteratively updated. Note that this will only give meaningful results if you in fact have a cluster. Luckily that can be checked afterwards using a trajectory viewer. Note also that if your molecules are broken this will not work either.

student0618 发表于 2026-1-6 14:17
明显是pbc的事，trjconv 用-pbc cluster 选复合物的组。

我想请教一下原理是什么嘞？我对pbc进行了-center -pbc mol -ur compact和-fit rot+trans

明显是pbc的事，trjconv 用-pbc cluster 选复合物的组。