increasing MAX_EXCLUSIONS

From: Francesco Oteri (francesco.oteri_at_gmail.com)
Date: Wed Jan 19 2011 - 16:07:05 CST

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
atoms.
When I try to minimize such a system with namd-gpu, I obtain the famous
error:

"........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?

Thanks,

                                                                                                         Francesco

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