xtc轨迹的pbc correction 失败

fantasticqhl · 发表于 Post on 2014-10-27 20:53:50

本帖最后由 fantasticqhl 于 2014-10-27 20:56 编辑

用MD 跑了一个16个氨基酸的多肽与1个Cu2+的dummy model的体系，Cu2+与多肽通过范德华与静电力相连。在得到轨迹之后，做了PBC correction。但是在某几个时间点，轨迹的Cu2+是在盒子的外面的。我的命令是： trjconv -f md.xtc -s md.tpr -pbc mol -ur compact -center -o md_correction.xtc 同时，我也试过-pbc的其它选项，nojump，whole，res等，还是不管用。在vmd里面，我用pbc plugin把Cu2+拉进盒子了，但是蛋白又出现了问题，有些原子跑到盒子外面去了，请问这样的问题如何解决呢，十分感谢呀！

如下图所示：

sobereva · 发表于 Post on 2014-10-27 21:08:12

没搞清楚你的情况。MD过程中氨基酸和Cu是一直在盒子中间区域呆着，还是跨越了盒子边缘？

fantasticqhl · 发表于 Post on 2014-10-27 21:19:31

谢谢sob！回复神速呀！

模拟过程中，蛋白与Cu都是呆在盒子中间的！

fantasticqhl · 发表于 Post on 2014-10-27 21:29:42

我再补充一点，我做的是REMD（explicit），可能是帧与帧之间跳跃比较大，用trjconv做correction就失败了！
我在NAMD的mailing list里面也找到了类似的一个邮件，我想我和他的问题是一样的！

From: Bob Johnson (robertjo_at_physics.upenn.edu)
Date: Thu Mar 15 2007 - 16:08:50 CDT

Hello everyone,
I'm trying to visualize/analyze the results of a replica exchange MD (REMD)
trajectory of a ssDNA molecule. The trajectory was calculated with Gromacs
which only writes the coordinates of atoms that are within the primary box. As
expected, during the trajectory, portions of the ssDNA that move into the next
periodic box are wrapped back into the primary box. As a result, the ssDNA
molecule appears to be broken and VMD draws long bonds from one end of the box
to the other.

Normally, I can correct for this using either the PBCtools unwrap plugin or the
Gromacs trjconv tool with the -pbc nojump option. However, the nature of the
REMD trajectory causes both of these options to fail.

I believe that the way both of these tools work is that they detect "jumps"
across the box and then correct for them by shifting the atoms back. These
"jumps" are simply large displacements between successive frames. However, in
REMD there are large displacements between successive frames due to the
instantaenous coordinate swaps. Thus, attempting to use the aforementioned
tools on a REMD trajectory leads to detection of erroneous "jumps".

I had the idea of writing a script that would remove PBC wrapping based on bond
length. If the bond in VMD gets larger than a certain amount, the script would
detect this as a jump. Then, the script would translate the appropriate atoms
in the appropriate direction to make the molecule whole again. I'm assuming VMD
stores information about what atoms share a "chemical bond" (i.e. are connected
by a line). Is there a way to access this information? My idea is still somewhat
rough so any suggestions or insights on this would be appreciated!
Thanks,
Bob Johnson

sobereva · 发表于 Post on 2014-10-27 21:44:59

如果把Cu的坐标往回挪一个周期的话位置是正确的，那就写个tcl脚本就好了。扫描每一帧，如果发现Cu的坐标超过了盒子边界，就把坐标减去盒子矢量。很容易实现

fantasticqhl · 发表于 Post on 2014-10-27 22:17:41

好的，谢谢sob！
我试试呀！

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[GROMACS] xtc轨迹的pbc correction 失败