[gmx-users] DPPS/Na in water system

[David L. Bostick]

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
 
processing coordinates...
double-checking input for internal consistency...

Granted this is a very tiny charge, why is it there?  How will it affect
calculation? 

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.

Thanks for any help,

David  

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	
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