Re: NAMD Error

From: Brian Radak (
Date: Tue Jul 17 2018 - 15:17:16 CDT

I frequently encounter similar problems with systems that size - most of
NAMD's performance heuristics are simply not designed for something small.

You can try increasing the margin (maybe 1 or 2?) or pairlistdist (16?
18?). You will probably also have less trouble without temperature control.

In general, I've never seen any stability benefit from heating a system
slowly versus all at once. There might be good reasons to heat a biopolymer
from a crystal structure, but for water this is almost certainly a waste of


On Tue, Jul 17, 2018 at 3:45 PM, Shriya Bansal <> wrote:

> Hello,
> I have been attempting to minimize and equilibrate a 38A TIP4P-2005 water
> box model built through CHARMM using the July 2017 TIP4P-2005 topology from
> The minimization for 2000
> steps has resulted in a trajectory file that exhibits no motion of the
> molecules. When this water box is that equilibrated, the error FATAL
> ERROR: Low global exclusion count! (5180 vs 5184) System unstable or
> pairlistdist or cutoff too small is produced. I have also commented out
> the heat up process and set the temperature to a constant value of 300K in
> attempt to counter this error. Please let me know potential sources of
> error within the minimization and equilibration steps.
> Best,
> Shriya Bansal

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