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

[Justin A. Lemkul]

sharada wrote:
> Hello,
> 
> 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.
> 

Several possibilities.  What parameters are you using for methanol?  Did you 
derive them yourself, or did you obtain them from somewhere else?

Also, you can consider using a newer (improved) force field, like Gromos96 53a6.

-Justin

> Thankyou in advance
> 
> sharada
> 
> 
> 
> 
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-- 
========================================

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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