[gmx-users] DPPS/Na in water system
David L. Bostick
dbostick at physics.unc.edu
Fri Apr 5 18:52:27 CEST 2002
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
double-checking input for internal consistency...
Granted this is a very tiny charge, why is it there? How will it affect
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 Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
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