[gmx-users] warning and PME

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 29 05:09:18 CET 2010

On 29/01/10 14:54, neo lotus wrote:
> Hi, while perform simulation, I perceive nether warning , I recourse
> page 87&147manual (PME part ),but I can 't understand that how apply
> change  in the  .mdp file according to said direction in the nether
> warning . please guide me, how remove error. consist warning :
>    Can not exclude the lattice Coulomb energy between energy groups

By its very nature, you can't exclude Ewald-style long-range Coulomb 
interactions between different groups. Perhaps some more background 
reading is in order. Then, reconsider your choice of the combination of 
PME and energy exclusions.


> Checking consistency between energy and charge groups...
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 42x42x125,
> 0.120 0.119 0.119
> NOTE 1 [file aminoacids.dat, line 1]:
>    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 2 Mb of data
> writing run input file...
> Thaks.

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