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Issue created by Paul Bauer@acmnpvMaintainer

trjconv produces gro files unreadable by VMD - Redmine #2037

Archive from user: Semen Yesylevskyy

Given tpr and pdb files attached I’m doing the following:

gmx trjconv -f for_eq.pdb -o trjconv.pdb 
gmx trjconv -f for_eq.pdb -o trjconv.gro

i.e. I’m just converting the same file for_eq.pdb to either pdb or gro.

When opening trjconv.gro in VMD it is corrupted completely, while trjconv.pdb is completely fine.

When I’m doing the same conversion with editconf the gro file IS readable:

gmx editconf -f for_eq.pdb -o editconf.gro # VMD is fine with this

The only difference between editconf.gro and trjconv.gro which I see is the number of decimal places:

trjconv.gro:
    1SM1      N    1   8.2780   8.3948   5.6172
editconf.gro
    1SM1      N    1   8.278   8.395   5.617

It seems that additional digits broke VMD gro files parser badly. This may be the bug in VMD rather than in Gromacs, but given the popularity of VMD it is better to make it happy.

The obvious solution is to make trjconv behave exactly as editconf.

(from redmine: issue id 2037, created on 2016-08-21 by gmxdefault, closed on 2016-09-08)

Remove variable precision gro writing

The gro precision is now fixed to 3, 4 and 5 decimal places for
x, v and box respectively to ensure compatibility with other software.
Variable precision reading is still supported.

Fixes #2037.

Change-Id: I0e593622ee0380c3934a7b7b6826ae29aed00a59
  • Revision 83192f1d by Mark Abraham on 2019-01-08T09:41:14Z:
Fix trjconv -ndec

This only works with XTC writing, but the documentation
and implementation was wrong. That mean that the terminal
feedback to the user was also wrong when writing a .gro file.

Fixes #2824
Refs #2037

Change-Id: I9f047d0b1042fa37e366ee8c99dabbb1f3458b0a
  • Revision cfb3ca1f by Mark Abraham on 2019-01-21T15:39:15Z:
Fix trjconv -ndec

This only works with XTC writing, but the documentation
and implementation was wrong. That mean that the terminal
feedback to the user was also wrong when writing a .gro file.

Fixes #2824
Refs #2037

Change-Id: I9f047d0b1042fa37e366ee8c99dabbb1f3458b0a