[gmx-users] DPPS/Na in water system

Erik Lindahl lindahl at stanford.edu
Fri Apr 5 19:48:43 CEST 2002

David L. Bostick wrote:

>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
>processing coordinates...
>double-checking input for internal consistency...
>Granted this is a very tiny charge, why is it there?  How will it affect
Hi David,

Actually I'm not sure it is there... The problem is that most atomic 
charges can't be
represented represented exactly in binary power-2 floating-point. This 
means there
is an error of about 1e-7 for each atom. When you add the charge from 
10000 atoms
or so, the error will increase as sqrt(N), so something around 1e-5 is 

Now, we never *use* this total charge in the simulation, and the error 
it might cause
in the PME routines is much lower than the inherent accuracy of PME 
which is around
1e-3 to 1e-4 depending on your grid spacing. I've seen exactly the same 
warning for
my uncharged DPPC molecules.

I actually halfheartedly tried to fix it once, but it's not trivial 
since it should depend on the system
size, but we still want to catch a unit charge in a very large system. 
Don't worry if it's 1e-5 though!

>I am also still interested in why the harmonic bonds in my system seem more
>stable in 3.0 (allowing me to take a 2 fs timestep) than in 3.1 (allowing
>only .1 fs timestep) during my bilayer construction.

This I'm not sure about - haven't had time to speak to Berk yet :-)



More information about the gromacs.org_gmx-users mailing list