[gmx-users] Change in structure after solvation_Gromacs

[ms]

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