[gmx-users] (no subject)

[Mónica Balsera]

Hi all, 
I am a new GROMACS user and I am trying to have a NMA of a protein. I would like to make you some questions. 
 Which parameters do you recommend to minimized for a further Normal Mode Analysis? I'd apprecite a lot if someone could send to me an example of the .mdp files. Might I do the energy minimization in water or in vacuum?
If the protein is charged, migth I include counter-ions for the minimization?? 
How large would be the Hessian matrix if the protein has 3500 atoms aprox? 
Thanks in advance for your kind attention, 
Best regards,

Monica

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