[gmx-users] error in PME mesh load

[Mark Abraham]

Hi,

Performance really doesn't matter for a typical energy minimization.
Running it probably takes less time than emailing :-)

Mark

On Mon, Dec 1, 2014 at 9:25 AM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> hello gromacs user
> i am working on complex with popc membrane i have problem in minimization
> step
> grompp -f minim1.mdp -c system_inflated.gro -p topol.top -o emr.tpr
> i got these notes how to adjust the load imbalance i red previous
> mails but it doesn't work my minimization file is
> define         = -DSTRONG_POSRES
> integrator    = steep
> emtol        = 1000.0
> emstep          = 0.01
> nsteps        = 50000
>
> nstlist        = 1
> ns_type        = grid
> rlist              = 1.2
> coulombtype    = PME
> rcoulomb        = 1.2
> rvdw               = 1.2
> pbc                = xyz
>
>
>  System has non-zero total charge: 13.999998
>   Total charge should normally be an integer. See
>
>
> Analysing residue names:
> There are:   408    Protein residues
> There are:   123      Other residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and
> splitting into groups...
> Number of degrees of freedom in T-Coupling group rest is 30828.00
> Largest charge group radii for Van der Waals: 0.252, 0.251 nm
> Largest charge group radii for Coulomb:       0.252, 0.251 nm
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 288x288x128, spacing 0.114 0.114 0.117
> Estimate for the relative computational load of the PME mesh part: 0.99
>
> NOTE 2 [file minim1.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
>
> kindly help
> --
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