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标题: 提取路径文件，trjconv运行出错 [打印本页]

作者
Author: hbyi 时间: 2022-3-18 16:57
标题: 提取路径文件，trjconv运行出错
  gmx_mpi trjconv -f envt3.xtc -s envt3.tpr -o envt-trj3.gro -b 0 -e 5000

Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write gro: Coordinate file in Gromos-87 format
Reading file envt3.tpr, VERSION 2021.4 (single precision)
Reading file envt3.tpr, VERSION 2021.4 (single precision)
Select group for output
Warning: file does not end with a newline, last line:

Group    0 (       System) has 13112 elements
Group    1 (       Other) has 13020 elements
Group    2 (          GC) has 900 elements
Group    3 (          CO) has 18 elements
Group    4 (          NA) has 20 elements
Group    5 (             K) has 20 elements
Group    6 (          CL) has 34 elements
Group    7 (          SOL) has 12120 elements
Group    8 (          CG) has 18 elements
Group    9 (          GC) has 900 elements
Group 10 (          CO) has 18 elements
Group 11 (          NA) has 20 elements
Group 12 (             K) has 20 elements
Group 13 (          CL) has 34 elements
Group 14 (          SOL) has 12120 elements
Group 15 (          NA) has 20 elements
Group 16 (          GC) has 900 elements
Group 17 (          CO) has 18 elements
Group 18 (          NA) has 20 elements
Group 19 (             K) has 20 elements
Group 20 (          CL) has 34 elements
Group 21 (          SOL) has 12120 elements
Group 22 (             K) has 20 elements
Group 23 (          GC) has 900 elements
Group 24 (          CO) has 18 elements
Group 25 (          NA) has 20 elements
Group 26 (             K) has 20 elements
Group 27 (          CL) has 34 elements
Group 28 (          SOL) has 12120 elements
Group 29 (          CL) has 34 elements
Group 30 (          GC) has 900 elements
Group 31 (          CO) has 18 elements
Group 32 (          NA) has 20 elements
Group 33 (             K) has 20 elements
Group 34 (          CL) has 34 elements
Group 35 (          SOL) has 12120 elements
Select a group:
-------------------------------------------------------
Program:    gmx trjconv, version 2021.4
Source file: src/gromacs/topology/index.cpp (line 902)

Fatal error:
Cannot read from input
For more information and tips for troubleshooting, please check the GROMACS

作者
Author: hbyi 时间: 2022-3-18 17:00
是还要读取一个ndx文件吗？我用make_ndx生成ndx文件也出现input error. 原子数多于10000，不是问题吧？

作者
Author: sobereva 时间: 2022-3-19 06:55

hbyi 发表于 2022-3-18 17:00
是还要读取一个ndx文件吗？我用make_ndx生成ndx文件也出现input error. 原子数多于10000，不是问题吧？

有别人回复之前若需要对帖子进行修改、补充，应直接编辑原帖，不要通过回帖进行补充，这点在置顶的新社员必读贴里明确说了。

说清楚trjconv启动后你都输入了什么

另外，-o接的是gro文件，很莫名其妙，你既然选取的不是单帧，干嘛用gro文件来记录，这比起xtc、trr格式大得多

作者
Author: hbyi 时间: 2022-3-19 09:52
本帖最后由 hbyi 于 2022-3-19 11:24 编辑

sobereva 发表于 2022-3-19 06:55
有别人回复之前若需要对帖子进行修改、补充，应直接编辑原帖，不要通过回帖进行补充，这点在置顶的新社员 ...

卢老师好，我是想提取为文本格式的坐标，然后用自己的代码分析动态信息，xtc、trr格式，我的分析小程序没法读xtc或trr格式，不清楚如何从xtc，trr中读出坐标参数。我在济南超算用脚本提交的，这是脚本中的作业运行。
mpirun -np 1 gmx_mpi traj -f envt2.trr -s envt2.gro -oxt coord.gro
所以运行后没有再输入参数。我提取一个shapshot的gro文件也出错。GROMACS:    gmx trjconv, version 2021.4
Executable: /es01/paratera/sce2051/soft/gromacs-install/bin/gmx_mpi
Data prefix:  /es01/paratera/sce2051/soft/gromacs-install
Working dir:  /es01/paratera/sce2051/work/grotest/gracoo
Command line:
  gmx_mpi trjconv -f envt3.trr -s envt3.tpr -o coord.gro -b 1000 -e 1000

Gromacs 2021.4的版本。我看了GROMACS 2022版，好像修复了trjconv的一些功能bug，但我没太弄清楚是否与我的我问题相关。
谢谢！

作者
Author: sobereva 时间: 2022-3-20 14:12

hbyi 发表于 2022-3-19 09:52
卢老师好，我是想提取为文本格式的坐标，然后用自己的代码分析动态信息，xtc、trr格式，我的分析小程序没 ...

VMD载入轨迹，保存成xyz轨迹格式，从中提取坐标很容易

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