[gmx-users] vacuum force field?

David van der Spoel spoel at xray.bmc.uu.se
Sat May 11 16:59:32 CEST 2002

On Sat, 11 May 2002, bxiong wrote:

>Dear User:
>I want to use the normal mode analysis to simulate a protein.I think it
>can not include the water. But I do not know how to select the force
>field. I use the vacuum force field.Is it correct? If it not, can you
>tell me how to do in the NMA simulation? 

You just run pdb2gmx and select the force field you want.
Then you do conjugate gradients minimization (needs double precision)
and then you run normal modes (set integrator to nm in mdp file).

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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