[gmx-users] cut-offs in j. kerrigans drug/enzyme tutorial

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 12 04:04:20 CEST 2007

merc mertens wrote:
> hello,
> looking at the mdp`s in the above named tutorial, one sees that in em, pr, md the rvdw (1.4 nm) is always bigger than the rcoulomb (1.0 nm). given that electrostatic interactions have a longer range than lennard-jones potentials i do not understand this choice. thanks for any help.

Hint: providing a link will help other people confirm what you're saying 
and/or find information to help answer your question.

I'd guess either the electrostatics are actually being treated with PME 
(and so rcoulomb is merely the direct-space cut-off), or that this was a 
design choice for a tutorial so that the calculation would finish 
quicker. The NAMD tutorials often have unphysically low cut-offs for 
this reason.

In choosing values for production simulations, you should be guided by 
the values for which the force field was parameterized, and by common 
practice from simulations reported in the last couple of years.


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