Is it possible to avoid printing extra comment lines at the end of .gro file?
Closed this issue · 2 comments
cihe13375 commented
Currently genice2 prints two extra lines at the end of .gro outputs. For example:
genice2 --water tip4p --rep 1 1 1 1h > test.gro
the content of test.gro is:
Generated by GenIce https://github.com/vitroid/GenIce
64
1ICE OW 1 0.127 0.183 0.337
1ICE HW1 2 0.175 0.149 0.261
1ICE HW2 3 0.175 0.149 0.413
1ICE MW 4 0.139 0.175 0.337
2ICE OW 5 0.528 0.447 0.106
2ICE HW1 6 0.570 0.481 0.185
2ICE HW2 7 0.438 0.482 0.109
2ICE MW 8 0.522 0.456 0.117
3ICE OW 9 0.659 0.539 0.331
3ICE HW1 10 0.656 0.634 0.334
3ICE HW2 11 0.613 0.510 0.410
3ICE MW 12 0.652 0.547 0.341
4ICE OW 13 0.528 0.449 0.556
4ICE HW1 14 0.438 0.484 0.560
4ICE HW2 15 0.570 0.483 0.636
4ICE MW 16 0.522 0.458 0.567
5ICE OW 17 0.256 0.091 0.563
5ICE HW1 18 0.261 -0.004 0.562
5ICE HW2 19 0.348 0.119 0.562
5ICE MW 20 0.268 0.083 0.563
6ICE OW 21 0.271 0.551 0.561
6ICE HW1 22 0.223 0.518 0.636
6ICE HW2 23 0.223 0.517 0.485
6ICE MW 24 0.259 0.542 0.561
7ICE OW 25 0.520 0.171 0.116
7ICE HW1 26 0.522 0.267 0.113
7ICE HW2 27 0.565 0.143 0.037
7ICE MW 28 0.526 0.180 0.106
8ICE OW 29 0.520 0.173 0.567
8ICE HW1 30 0.565 0.144 0.488
8ICE HW2 31 0.523 0.269 0.563
8ICE MW 32 0.526 0.182 0.556
9ICE OW 33 0.140 0.461 0.786
9ICE HW1 34 0.137 0.365 0.787
9ICE HW2 35 0.049 0.489 0.786
9ICE MW 36 0.128 0.452 0.786
10ICE OW 37 0.140 0.459 0.336
10ICE HW1 38 0.049 0.487 0.336
10ICE HW2 39 0.137 0.364 0.336
10ICE MW 40 0.128 0.451 0.336
11ICE OW 41 0.271 0.549 0.110
11ICE HW1 42 0.223 0.516 0.186
11ICE HW2 43 0.223 0.516 0.034
11ICE MW 44 0.259 0.540 0.110
12ICE OW 45 0.256 0.089 0.112
12ICE HW1 46 0.261 -0.006 0.111
12ICE HW2 47 0.348 0.118 0.112
12ICE MW 48 0.268 0.081 0.112
13ICE OW 49 0.649 0.079 0.342
13ICE HW1 50 0.738 0.114 0.339
13ICE HW2 51 0.607 0.113 0.263
13ICE MW 52 0.655 0.088 0.331
14ICE OW 53 0.649 0.081 0.792
14ICE HW1 54 0.607 0.115 0.713
14ICE HW2 55 0.738 0.116 0.789
14ICE MW 56 0.655 0.090 0.782
15ICE OW 57 0.659 0.541 0.781
15ICE HW1 58 0.655 0.636 0.785
15ICE HW2 59 0.613 0.512 0.860
15ICE MW 60 0.652 0.549 0.792
16ICE OW 61 0.127 0.185 0.787
16ICE HW1 62 0.174 0.150 0.863
16ICE HW2 63 0.175 0.151 0.712
16ICE MW 64 0.139 0.176 0.787
0.78228388 0.73535726 0.90365185
#
#Command line: c:\users\username\appdata\local\programs\python\python38\scripts\genice2 --water tip4p --rep 1 1 1 1h
The two extra lines at the end breaks some tools, such as trjconv coming from Gromacs itself:
> gmx -quiet trjconv -f .\test.gro
Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading frames from gro file 'Generated by GenIce https://github.com/vitroid/GenIce ', 64 atoms.
Reading frame 0 time 0.000 Reading frames from gro file 'Generated by GenIce https://github.com/vitroid/GenIce ', 64 atoms.
Reading frame 0 time 0.000
Precision of .\test.gro is 0.001 (nm)
Using output precision of 0.001 (nm)
-> frame 0 time 0.000
-------------------------------------------------------
Program: gmx trjconv, version 2020.6-MODIFIED
Source file: src\gromacs\fileio\groio.cpp (line 67)
Fatal error:
gro file does not have the number of atoms on the second line
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Deleting the two extra lines fix the issue.
Of course I can always delete them manually, but that is a bit annoying :(
vitroid commented
Thank you for your opinion! You are right.
I modified not to output the comment at the bottom of .gro file and deployed as the newest version 2.1.7.1.
Could you please re-install it with pip command?
cihe13375 commented
Thanks for the fix! Can confirm it resolves the issue.