[gmx-users] PME error for energy minimization of TMD in lipid bilayer
jalemkul at vt.edu
Fri Oct 5 12:06:47 CEST 2012
On 10/5/12 5:20 AM, Archana Sonawani wrote:
> 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?
That is not an error, it's a precautionary note. For EM, the PME load is
largely irrelevant. With an inflated system that is very large, you're going to
(by necessity) have a massive PME grid.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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