Upon executing Heating.conf file the log file generated reads "Warning: Low global CUDA exclusion count ! (54185 Vs 54329) System unstable or pairlistdist or cutoff too small. There are no calculations recorded in the log file, tried ploting in the VMD's NAMD plot, shows " Error: floating point value is Not a Number". I tried with modified pairlistdist and cutoff and even did not use "idlepoll" (as it wont deploy GPU). But still got the same result in the log file.
Heating and Equilibration are crucial steps as per the research methodology. Would appreciate any suggestions. I have uploaded heating conf. and log files and minimization files as well .
Thank you
Diptesh Das I recently had the same issue and received the error message "FATAL ERROR: Low global exclusion count! (30419 vs 30420) System unstable or pairlistdist or cutoff too small." in the log file. I have played around with pairlistdist and cutoff but no luck. Could you share how you solved the problem? Thanks!
As you've said you adjusted pairlist and cutoff. Hence
This problem could arise due to unupdated conf. or namd. files where coordinated and velocities are not set as the previous run output. Please check if they are written in binary or you have mentioned "bin" before the coordinate and velocities entry. or
check if cuda cores are well integrated with your MD engine.
Diptesh Das Fangfang Zhong Vinay Thakur I encountered the same error.
FATAL ERROR: Low global exclusion count! (2505 vs 2581) System unstable or pairlistdist or cutoff too small.
Can you please clarify how to solved this?
Kindly increase minimization steps to 20,000 to 30,000. I solve this problem by this which is caused by improper protein structure.
Hi everybody,
I also had this error and so that solved by studying of the pdf file of NAMD User’s Guide (Version CVS-2012-04-16-----page 82). You can download it free in google.
Solution:
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.
I hope this can be helpful :)
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