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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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