[gmx-developers] Exclude specific nonbonded interactions during md rerun for Verlet

Berk Hess hess at kth.se
Fri Sep 12 16:21:13 CEST 2014


Why do you need to exclude energy group interactions during rerun?
Since you will have all the energy group pair contributions you can 
manually subtract the terms you want to exclude. You wouldn't even need 
a rerun for that if you used the energy groups for the production run.



On 09/12/2014 03:26 PM, Bernd Doser wrote:
> Dear GROMACS developers,
> As the energy group exclusions are not implemented for the Verlet cutoff
> scheme, I am search for a alternative possibility to exclude specific
> nonbonded interactions during an md rerun.
> One idea is to use the topology exclusion list. The top->excl arrays
> could be modified for example at the beginning of do_force() in
> sim_util.c. I have tested it for a small protein and a water dimer and
> it works. Is there any problem doing this for more complex structures or
> have anyone a better idea to exclude nonbonded interactions to reduce
> computation time?
> Thank you very much in advance!
> Best regards,
> Bernd Doser

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