[gmx-users] error in PME mesh load

RINU KHATTRI nickname.mittu at gmail.com
Mon Dec 1 09:25:48 CET 2014

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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