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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