System net charge

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Fri Jul 29 2011 - 03:25:11 CDT

Dear NAMD Users:
 
I built a system with a dppc lipid bilayer plus water. But I got the following mistake:

 
 Autoionize) System net charge after adding ions: -2584.480033516884e
WARNING: System has a non-integer total charge. There was likely a problem in the process of building it.
 
 
Is it correct that the system has this amount of charge?
 
The script I used was:
 
########################################################################
mol new dppc.psf
 mol addfile dppc.pdb
 
package require solvate
solvate dppc.psf dppc_tem.pdb -z 5 +z 50 -o dppc_water
 
 
set sel [atomselect top all]
     set netCharge0 [eval "vecadd [$sel get charge]"]
     $sel delete
 
### Neutralizar el sistema: añadimos 8 iones Cl y 4 iones Na. Y calcular la carga neta del Nuevo sistema
 resetpsf
 package require psfgen
 package require autoionize
  
autoionize -psf dppc_water.psf -pdb dppc_water.pdb -nna 4 -ncl 8
 
###########################################################################
 
I also used the dppc files (pdb and psf) from membrane tutorial files of NAMD. (http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/)
 
 
Thanks for your help
 
 
 Hernán Andrés Morales Navarrete

Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253
http://www.ciencias.epn.edu.ec/~biomod/

 
                                                

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