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

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 13 04:53:13 CEST 2012

On 7/12/12 10:23 PM, J Peterson wrote:
> 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

Assuming this is the net charge on your protein, there's nothing wrong here.

> 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

PME load for EM runs is usually irrelevant.  During actual MD, you'd strive for 
better balance, but since an inflated lipid system in vacuo is rather weird, you 
can ignore this as well.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list