GROMACS version: 2021
GROMACS modification: Yes/No
Here post your question
Hi i am using gromacs 2021. i want to perform pca analysis but getting this error.
“Range checking error (possible bug):
The provided structure file only contains 59387 coordinates, but coordinate
index 3864 was requested for fitting. Make sure to update structure files and
index files if you store only a part of your system.”
please help me out if this could be resolve.
Could you share what commands you entered to get to this error?
i tried these two
gmx covar -s md_100.gro -f md_noPBC.xtc -o eigenvalues.xvg -v eigenvectors.trr -xpma covar.xpm
gmx covar -s md_100.tpr -f md_noPBC.xtc -o eigenvalues.xvg -v eigenvectors.trr -xpma covar.xpm
both times same error.
If you’re following the manual, the gmx covar step involves generating “a reference file (tpr, gro, pdb etc.) containing the same number of “atoms” as the new trr file, that is for n dihedrals you need 2n/3 atoms (rounded up if not an integer number)”. So you can take any pre-existing .gro file and delete all but 2n/3 atoms (doesn’t matter which atoms as long as the number of atoms match), then use that .gro file for the gmx covar command along with the -nofit option.
Also, the -f option should be the .trr you generated from the previous step