From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 19 2011 - 16:42:29 CST
On Wed, Jan 19, 2011 at 5:07 PM, Francesco Oteri
> Dear namd users,
> I need a suggestion regarding increasing of MAX_EXCLUSIONS variable.
> In particular, I need to simulate a system composed by about 1.100.000
> When I try to minimize such a system with namd-gpu, I obtain the famous
> "........Increase MAX_EXCLUSIONS."
> In the file ComputeNonbondedCUDAKernel.h, the value of MAX_EXCLUSIONS is
> 2048. I increased this value to 6144 (1024*6) and the compilation has been
> succesfully completed, but when I run a minimization with constrain on
> Protein-DNA atoms,
> NAMD destroys the protein increasing the lenght of the covalent bonds.
> The CPU version doesn't show this behaviour.
> I think that simply increasing MAX_EXCLUSIONS is not enough :)
> Does anyone have a solution to the problem?
an explanation and a suggestion for a workaround was
given on this very list less than a week ago.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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