[gmx-users] truncated LJ potential

Makoto Yoneya makoto-yoneya at aist.go.jp
Fri Jan 28 07:24:38 CET 2011

Dear Mark and all:

Dr. Mark Abraham wrote:
> > and set the environment variable?
> You'd only have learned to do this if you'd used a debugger to step 
> through the flow of the code. I highly recommend that procedure. 
> init_forcerec() checks an environment variable and triggers the use of 
> generic kernels accordingly. Various other environment variables have 
> various other effects there and deeper in the code.
Thanks a lot of the great info.
I'd found the environment variable is GMX_NB_GENERIC.
By setting this, my modification code was activated and the LJ potential
outputs were turned from negative to positive values (since the LJ was
truncated till its repulsive part).

> > How can I do the recognision
> Find the part of the code that triggers that error message, examine what 
> circumstances and data structures trigger it and modify suitably. Then 
> look where else that data structure is used and adapt as necessary.
For this, I still could not figured out.
The variable eNBF_NR limits the case number in the routin topio.c, but
I could not find how the variable was defined.
I'll try more.

Thanks a lot again.

Makoto Yoneya, Dr.

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