GROMACS version: 2021.2
GROMACS modification: No
Here post your question
I have indexing issue in the xtc file format.
my topol.to top file has the following items:
; Compound #mols
IAUM 18642
protein XXXX; i have intentionally changed the Proteins to XXXX
W 3798848
NA 1714
in the mdp file, I try to just output my NP, protein and ions in the xtc file:
nstxtcout = 10000 ; Output frequency for .xtc file
xtc_precision = 100
xtc-grps =IAUM-Pro-ion ;IAUM protein IONs_all
to do so, I make a group in my index file called “IAUM-Pro-ion”. I also double checked to make sure the index numbers do match and I only have IAUM, protein and ION in the system!
However, when I try to use trjconv to convert xtc to gro file, using the same index file and the same group as shown below ( Group 18 ( IAUM-Pro-ion) has 444023 elements ), I get error of mismatching numbers.
gmx trjconv -f nvt-production-30fs.xtc -s nvt-production-30fs.tpr -o nvt-production-30fs-c.gro -pbc mol -n index.ndx
:-) GROMACS - gmx trjconv, 2021.2 (-:
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GROMACS: gmx trjconv, version 2021.2
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/mkhatami/uoft/gromacs/Au-C6-1ao6-1hzh-1d3k/all-elastic/full-structures/80nmbox/006-nvt-production-large-freeze
Command line:
gmx trjconv -f nvt-production-30fs.xtc -s nvt-production-30fs.tpr -o nvt-production-30fs-c.gro -pbc mol -n index.ndx
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 nvt-production-30fs.tpr, VERSION 2021.2 (single precision)
Reading file nvt-production-30fs.tpr, VERSION 2021.2 (single precision)
Select group for output
Group 0 ( System) has 4242871 elements
Group 1 ( Other) has 3819204 elements
Group 2 ( IAUM) has 18642 elements
Group 3 ( W) has 3798848 elements
Group 4 ( ION) has 1714 elements
Group 5 ( Protein) has 423667 elements
Group 6 ( Protein-H) has 423667 elements
Group 7 ( C-alpha) has 0 elements
Group 8 ( Backbone) has 0 elements
Group 9 ( MainChain) has 0 elements
Group 10 ( MainChain+Cb) has 0 elements
Group 11 ( MainChain+H) has 0 elements
Group 12 ( SideChain) has 423667 elements
Group 13 ( SideChain-H) has 423667 elements
Group 14 ( Prot-Masses) has 423667 elements
Group 15 ( non-Protein) has 3819204 elements
Group 16 ( W_ION) has 3800562 elements
Group 17 ( IONs_all) has 1714 elements
Group 18 ( IAUM-Pro-ion) has 444023 elements
Group 19 ( IAUM-Pro-modif) has 442339 elements
Select a group: 18
Selected 18: 'IAUM-Pro-ion'
Reading frame 0 time 0.000
Precision of nvt-production-30fs.xtc is 0.01 (nm)
-------------------------------------------------------
Program: gmx trjconv, version 2021.2
Source file: src/gromacs/tools/trjconv.cpp (line 921)
Fatal error:
Index[442309] 4241158 is larger than the number of atoms in the
trajectory file (444023). There is a mismatch in the contents
of your -f, -s and/or -n files.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
The interesting part is that when I make an new group (Group 19 ( IAUM-Pro-modif) has 442339 elements) including some water indices and removing the ions the code creates the gro file.
Is it a bug in the grompp? or am I doing something wrong?
Best,
Mohammad