[gmx-users] truncated LJ potential

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 28 06:24:51 CET 2011

On 28/01/2011 3:44 PM, Makoto Yoneya wrote:
> Dear Mark and all:
> Dr. Mark Abraham wrote:
>> So you have to update the machinery that parses the .top to recognise
>> that the value of 4 is now legal.
> and also
>> Did you set the environment variable to actually call the generic
>> nonbonded lists?
> Thanks a lot for your comments.
> I did not care these at all.
> Which part of the manual contain the info?

None. Unfortunately, not everything that every developer might want to 
know for every project can be documented.

> (I'd tried a search in the GROMACS web page, but I could not find that.)
> 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.

> 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.


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