[gmx-users] mixed solvent density

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Sun Aug 1 08:51:02 CEST 2004

Dear John,
I just wrote you an email about this solvent mixture. My strong advice 
is not to use it. You probably read the papers by Kessler and 
coworkers. I actually did some of the NMR experiments with EmrE in this 
solvent mixture, and I have all reasons to believe that the protein is 
not folded under these conditions. There is secondary structure 
(probably even the native one), but the helices are floating apart. The 
main difference between this solvent mixture and a membrane is that 
Chloroform/methanol/water is more or less isotropic, so you loose all 
the directional information from the membrane. You really should use 
something else. There are some papers by Mierke, who used 
water/decane/water. Though also problematic, it's much better. He also 
has an equilibrated box. Or ask around for the water/argon/water box. 
Both systems make much more sense.
Good luck,

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