[gmx-users] Change in structure after solvation_Gromacs

[swagata chakraborty]

Hi,

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.


Regards
Swagata Chakraborty
Research Scholar,
Department of Chemical Sciences,
Tata Institute of Fundamental Research,
Mumbai-400005
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