[gmx-users] Protein segment

Marc Ceruso mceruso at physbio.mssm.edu
Thu Sep 11 21:58:01 CEST 2003


>  How can I do(If it's posible) a simulation of a protein in water whith
> a segment(for example residue 20-50) that not move, and the others free
> of movment

There is more than one way to do this but for a quick set up you can use
restraints (via posre.itp, -DPOSRES in .mdp and -r option in grompp)
in this case the atoms are not completely fixed (it depends on the force
constant you define in posre.itp), alternatively if you want
them completely fixed you can use freeze groups in .mdp

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