[gmx-users] PME error for energy minimization of TMD in lipid bilayer

Archana Sonawani ask.archana at gmail.com
Fri Oct 5 11:20:08 CEST 2012

Dear gromacs users,

I am energy minimizing the TMD (286 residues) in lipid bilayer for
inflategro step. I am getting the following error.

Analysing residue names:
There are:   287    Protein residues
There are:   127      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 28464.00
Largest charge group radii for Van der Waals: 0.248, 0.247 nm
Largest charge group radii for Coulomb:       0.248, 0.247 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 320x320x60, spacing 0.111 0.110 0.115
Estimate for the relative computational load of the PME mesh part: 0.98

NOTE 2 [file EM.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

The em.mdp file is as follows:
title           = EM of TMD-POPC system
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

Can any one suggest me what changes should I make for my large system?
Thanks in advance


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