Hi, Tom
Thanks very much for your reply. As you said, I was running a 100ps equilibration of the density where the system density was increased during the run. As you explained, I now understand that the problem is that at some point of the run the list of direct sum dipole-dipoles exceeds the initial allocated size.
I have restarted with the same cutoff as before and it works. Thanks again for your explaination and help!
Sincerely
Zhen
________________________________________
From: owner-amber.scripps.edu [owner-amber.scripps.edu] On Behalf Of Tom Darden [darden.niehs.nih.gov]
Sent: Monday, September 22, 2008 4:51 PM
To: amber.scripps.edu
Subject: Re: AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba.
Dear Zhao
The message is a bit confusing---its a list that stores the direct sum
dipole-dipole interactions (instead of recalculating them) during the
induction iterations---that is allocated.
This list is allocated at the initialization of the run, based on how many
nonbond pairs are found then. If the number of such pairs increases
during the run---say due to increased system density--it may be too small
at some point.
The easiest thing is to restart the simulation with the same cutoff as
before.
If you get this problem after stabilization of the system density--please
email again--a bug is always possible
tom d
On Mon, 22
Sep 2008, Zhao, Zhen (zhaozh) wrote:
> Hi, all
>
> I started a simulation using Amoeba force field in Amber 10. The simulation stopped after running about 30ps and complained about
> " Too many dipole-dipole interaction allocated".
>
> I donot know what the problem is. Should I make the cut-off smaller ? Thanks in advance!
>
> Sincerely
>
> Zhen
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Received on Wed Sep 24 2008 - 05:10:00 PDT
