[gmx-users] DPPS/Na in water system

Marcos Villarreal arloa at dqb.fcq.unc.edu.ar
Fri Apr 5 21:56:46 CEST 2002

On Friday 05 April 2002 01:52 pm, you wrote:
> Hello,
> I have written emails earlier about equilibration of a DPPS bilayer from
> scratch.  I have gromacs 3.0 installed in single precision and am running a
> bilayer with 2624 waters , 128 sodiums, and 128 DPPS molecules.
> The topology for a DPPS molecule has a net charge of EXACTLY -1.  So the
> entire system should have a net charge of exactly zero because of the
> Sodium counterions.  However upon grompp, I get,
> checking input for internal consistency...
> Excluding 3 bonded neighbours for DPS 128
> Excluding 2 bonded neighbours for SOL 2624
> Excluding 1 bonded neighbours for NA 128
> Warning 1 [file "../ps.top", line 22]:
>   System has non-zero total charge: 2.437830e-05

I have noticed this in others lipid/water/whatever systems, when using 
-shuffle. Whitout -shuffle in grompp, the error disappear. Besides this 
warning the simulations with PME were stable in runs up to 100 ns.


Marcos Villarreal
Grupo de Biofisica
Departamento de Quimica Biologica - CIQUIBIC.
Universidad Nacional de Cordoba.
Cordoba. Argentina.

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