On 05/12/10 10:39, swagata chakraborty wrote:
I was trying to run MD simulation of my protein in DMSO. I used the force
field ffG53a6 and did the energy minimization after solvating the protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the loop at the dimer interface is converting into a sheet.
Please suggest where I am going wrong since the structure shouldnot change
after solvation.
You're not giving nearly enough detail (what is the dmso/water ratio?
what is your .mdp file?) etc.
In any case, it wouldn't be the first time that simulations and
experiments disagree. How do you *know* that structure shouldn't change?
Have you tried using another force field, like OPLS?
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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