[gmx-users] (no subject)
mbalsera at airtel.net
Thu Feb 13 20:40:39 CET 2003
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,
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