[gmx-users] genion problem with large systems

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 9 15:36:34 CEST 2008

Hi all,

I'm experiencing a strange problem with genion that I have never seen before.  I 
am preparing some membrane systems, many of which involve a large number of 
charged lipids (several hundred).  When using lipids with PC headgroups (no net 
charge), the following works fine:

genion -s ions.tpr -o system_solv_ions.gro -pname NA+ -nname CL- -neutral -conc 0.15

The only charged species is the embedded protein (-3 net charge).  However, if I 
process a system containing, for example, 512 POPG lipids, genion (with the same 
command given above), always leaves the system with a net +2 charge.  Even if I 
change -rmin (down to 0.1) or -seed, I get the same result, always a net +2. 
Obviously, I can fix this with another round of genion, but I was curious to see 
if there was some reason genion fails with the above command for systems with 
large numbers of charged species.  I am using GMX 3.3.3.

Thanks for your attention.



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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