[gmx-users] Re: Error in Membrane simulations with POPC bilayer

J Peterson think_beyond at aol.com
Fri Jul 13 04:23:39 CEST 2012

Hi Justin, 

Thanks for the suggestion I got it solved somehow. The main problem was in
the popc128b.pdb itself, it has first 64 lipids and half of the SOl
molecules followed by rest of the POPC and SOL molecules. When I rearranged
them the error was solved.

But now another thing I would like to confirm with you. During shrinking
stage, I get the following notes, please tell me are they OK at this stage,

NOTE 1 [file topol.top, line 3070]:
  System has non-zero total charge: 5.000000e+00

Analysing residue names:
There are:    46    Protein residues
There are:   126      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 21063.00
Largest charge group radii for Van der Waals: 0.249, 0.247 nm
Largest charge group radii for Coulomb:       0.249, 0.247 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 160x160x48, spacing 0.110 0.114 0.119
Estimate for the relative computational load of the PME mesh part: 0.92

NOTE 2 [file em_st.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

This run will generate roughly 17 Mb of data

There were 2 notes

Peterson J

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