Do you know that facing types of errors during doing projects is the best way to understand and improve your skills for your professional future 🙂
SO, some of the usual errors from my experiences with molecular dynamics simulations are here for you my friends and I hope they can be helpful 🙂
- NAMD & VMD:
High global exclusion count, FATAL ERROR: High global exclusion count! (2505 vs 2581) System unstable or pairlistdist or cutoff too small
I also had this error and so that was solved by studying the pdf file of NAMD User’s Guide (Version CVS-2012-04-16—–page 82). You can download it free on google.
If an “atoms moving too fast; simulation has become unstable”, “bad global exclusion count”, or similar error happens on the first timestep then there is likely something very wrong with the input coordinates, such as the atoms with uninitialized coordinates or different atom orders in the PSF and PDB file.
So I checked my atom numbers and orders in pdb and psf files and they were not the same so I edited my PDB file and create my PSF file again and finally, it got correct and run done.
And it may be due to the overlapping of the atoms, and once when I changed the dimensions of the simulation box, followed by a change in the coordinates of the atoms, it was solved.
FATAL ERROR: ABNORMAL EOF FOUND – buffer=*F
EOF= End Of File & it shows maybe the end of input files like param, so you just can do it by some click on Inter and create some empty line after your end of the file, simply 🙂
This page become updating and the next errors will add here.