[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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