[gmx-users] energy minimization_note

[Mark Abraham]

Hi,

Do check out the PME tuning sections in the reference manual. But typically
EM in vacuum is short enough you should not consider optimizing it. (And
mdrun should perhaps not issue such notes / as liberally.)

Mark

On Wed, Jul 18, 2018 at 5:36 PM Atila Petrosian <atila.petrosian at gmail.com>
wrote:

> Dear gromacs users,
>
> I am doing md simulation of cnt + drug + water molecules. The em.mdp file
> is follows:
>
> integrator               = steep
> nsteps                   = 50000
> emtol                    = 10
> emstep                   = 0.01
> ns_type                  = grid
> rlist                      = 1.0
> coulombtype              = PME
> Cutoff-scheme            = Verlet
> vdwtype                  = Cut-off
> rcoulomb                 = 1.0
> rvdw                     = 1.0
> constraints              = none
> periodic_molecules       = yes
>
> ---------------------------------------------------
>
> After using ( gmx_mpi grompp -f em_vac.mdp -c complex.gro -p topol.top -o
> em_vac.tpr),
>
> NOTE 1 [file em_vac.mdp]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing.
>
> -----------------------------------------------------
>
> Are these parameters true?
>
> Which changes I should consider in this mdp file to have not this note?
>
> Which cut-off is appropriate?
>
> Best,
> Atila
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