From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue Sep 02 2014 - 17:27:20 CDT
Sounds like there’s a geometric problem (atoms overlapping, an overlong bond, an angle way off from norm...) somewhere in your protein, which will cause a crash like this on startup. This is why you should always perform a second minimization with the protein atoms free before starting full dynamics. A fairly typical protocol is:
- Minimize for a few thousand steps (25,000 is usually overkill) followed by ~20,000 steps of MD, all with protein atoms either fixed or restrained. This allows the water to thoroughly “soak” the protein before you start it moving.
- Minimize for another few thousand steps with the protein free to move. This relaxes any “bad” geometrical features in the starting structure, so that it will start gracefully. Note that it’s always a good idea to check out any bad areas for yourself (running the structure past a server such as Molprobity will give you an exhaustive list) before you actually go ahead – it’s quite common for existing crystal structures to have quite serious errors which will badly bias your simulation.
- Finally, start your MD run. Some people choose to run a protocol of gradually heating the system up from 0 to 300K – personally, I don’t find that makes much of a difference in most cases.
Hope this helps.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Sandhyaa Subramanian
Sent: Sunday, 31 August 2014 12:06 AM
Subject: namd-l: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small.
I encountered the following error while trying to equilibrate my system which is a protein solvated with 7A water box and minimized with 25,000 steps -
FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small.
I tried changing the pairlistdist to 15.0 and the cutoff to 13.0, but in vain. I do not understand why the atom names are mentioned because when I checked the psf files they seem Ok to me. Also the protein was fixed during the minimization.
Please help at your earliest.
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