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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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