[gmx-users] Melittin in Methanol.......

sharada sharada at ccmb.res.in
Thu Jan 29 14:02:58 CET 2009

I am doing a simulation  of melittin molecule in methanol box for 3 ns. I am finding that it is unfolding very rapidly and is behaving more like in water. 
Melittin behaviour in water, methanol and also in lipids is well documented and known since quite some time. I am using the methanol216.gro provided along with gromacs software. I am using ffG43a3 force field. The density of methanol is around 771.238 g/l.  The backbone rmsd shoots up to 0.5nm immediatly after 500 ps which  indicates that it is unfolding. I have no clue why it is behaving in this manner.  Melittin unfolds in water like this but not in methanol. Can any one tell me where I am going wrong. Any insight in this direction is welcome.
Thankyou in advance
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