Yes it should be fine for it to be applied after equilibration - you are running with shake so the X-H bonds are not a degree of freedom. Remember to modify your prmtop with parmed though before increasing the timestep.
All the best
Ross
> On Jun 9, 2015, at 11:09 AM, Parker de Waal <Parker.deWaal.vai.org> wrote:
>
> Hi Everyone,
>
> With regards to hydrogen mass partitioning, can this be applied after the system has been equilibrated (i.e. only perform production simulations with HMR) or should the entire simulation pipeline (minimization -> heating -> pressure -> prod) be run with HMR?
>
> Best,
> Parker
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Received on Tue Jun 09 2015 - 12:00:03 PDT
