求助轨迹中双链蛋白分离，并越过盒子

chenbq18 · 发表于 Post on 2022-1-7 15:06:32

请教各位老师，双链蛋白的模拟，在equil过程中发生了越过盒子，分离的现象，但未能提前发现。直接做了MD。在MD过程中虽然设置消除了平动转动，但轨迹依然是越过盒子了。
尝试用manual上的方法（如下），并不work！
是与标红的部分有关吗？不是很理解这个意思。
谢谢！

Fixing periodicity effects with gmx trjconv to suit visualization or analysis can be tricky. Multiple invocations can be necessary. You may need to create custom index groups (e.g. to keep your ligand with your protein) Following the steps below in order (omitting those not required) should help get a pleasant result. You will need to consult gmx trjconv -h to find out the details for each step. That’s deliberate – there is no magic “do what I want” recipe. You have to decide what you want, first. :-)

First make your molecules whole if you want them whole.
Cluster your molecules/particles if you want them clustered.
If you want jumps removed, extract the first frame from the trajectory to use as the reference, and then use -pbc nojump with that first frame as reference.
Center your system using some criterion. Doing so shifts the system, so don’t use -pbc nojump after this step.
Perhaps put everything in some box with the other -pbc or -ur options.
Fit the resulting trajectory to some (other) reference structure (if desired), and don’t use any PBC related option afterwards.

With point three, the issue is that gmx trjconv removes the jumps from the first frame using the reference structure provided with -s. If the reference structure (run input file) is not clustered/whole, using -pbc nojump will undo steps 1 and 2.

Alpaca · 发表于 Post on 2023-3-31 13:53:44

请问楼主解决了吗？这个问题

Alpaca · 发表于 Post on 2023-3-31 13:42:22

本帖最后由 Alpaca 于 2023-3-31 13:56 编辑

chenbq18 · 发表于 Post on 2022-1-8 10:40:33

sobereva 发表于 2022-1-8 10:08
我不知道你怎么定义的组
搞清楚-pbc cluster的用处和用法，结合实际情况判断怎么回事

把两条链所有的残基定义成一个组，是这个问题吗

sobereva · 发表于 Post on 2022-1-8 10:08:42

chenbq18 发表于 2022-1-8 09:05
试了cluster方法，还是不行呢？
gmx editconf -f ../topology/3b.gro -o 3b_box.gro -d 1.0 ,这样设置的 ...

我不知道你怎么定义的组
搞清楚-pbc cluster的用处和用法，结合实际情况判断怎么回事

chenbq18 · 发表于 Post on 2022-1-8 09:05:40

sobereva 发表于 2022-1-8 06:03
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-271 ...

试了cluster方法，还是不行呢？
gmx editconf -f ../topology/3b.gro -o 3b_box.gro -d 1.0 ,这样设置的box，应该没问题啊。box的大小不是自动根据蛋白大小决定的吗，边界1.0nm也正常呢

sobereva · 发表于 Post on 2022-1-8 06:03:15

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）
里面提了用-pbc cluster处理可以解决

另外，我感觉你这盒子设得太小

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[GROMACS] 求助轨迹中双链蛋白分离，并越过盒子

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