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<P>Hi all, <BR>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. <BR> 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?<BR>If the
protein is charged, migth I include counter-ions for the minimization?? <BR>How
large would be the Hessian matrix if the protein has 3500 atoms aprox?
<BR>Thanks in advance for your kind attention, <BR>Best regards,</P>
<P>Monica</P></FONT></DIV></BODY></HTML>