[gmx-users] PBC

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 8 10:37:39 CEST 2015


On Thu, Oct 8, 2015 at 8:08 AM mah maz <mahmaz71 at gmail.com> wrote:

> Hi Mark
> Thank you. I suppose grid can be used without PBC specially when the system
> is in vacuum.
> There are some parameters in the .mdp file that I haven't defined and I
> don't want them to be applied during simulation. However in the mdout.mdp
> They are present eg. gen-seed, emtol, ewald-rtol,.... Do they play a role
> in the simulation?

Yes, gen-seed kills a kitten and ewald-rtol launches nuclear missiles ;-)
(Stuff that configures inactive algorithms isn't active.)


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