Re: problem about pairlistdistance...

From: Peter Freddolino (
Date: Tue Apr 10 2007 - 13:39:39 CDT

Hi Harish,
anything in info tags, including this, is generally not considered
harmful; indeed, I don't think this output is normally even given in
NAMD 2.6. What this particular message means is that NAMD tried to
dynamically shrink your pairlist distance to speed computation, found
that such a change could cause problems, and backed off. It shouldn't
have any effect on dynamics. However, it is odd that this doesn't show
up until step 100000. Is there anything unusual about your simulation
(e.g., is it in gas phase?) What time step are you starting it?
You can enforce some extra padding on the pairlist distance by adding a
nonzero margin if this bothers you.
Peter wrote:
> Hi All,
> In my NVE simulation log file, i am getting some warnings about pairlistdistance parameter as:
> info:Pairlistdist is too small for 20 patches during timestep 100000
> I looked through namd users guide and tutorial which tells it can be due to small pairlistdist or long cycle. My parameters are as follows:
> cutoff 12
> switchdist 10
> pairlistdist 16
> steprspercycle 10
> As far as i know ~"4A" is enough cushion between cutoff and pairlistdist to account for all pairs. Before I had set it to 14 but increased to 16. Still, these info:(warnings) haven't stopped. I tried changing cycle which didnt help either.
> If someone has more experience in playing around with them, Please advise.
> Thanks
> Harish
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823

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