[gmx-users] movement in 2 directions - remove one degree of freedom

[Oliver Stueker]

Hi,

as an alternative of applying position restraints to only the y-component,
one can also define a freeze-group only to act on the Y-axis by using:

freezedim N Y N

see: http://manual.gromacs.org/online/mdp_opt.html#neq  freezegrps and freezedim

Oliver

On Fri, May 11, 2012 at 7:39 AM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>
> 11 maj 2012 kl. 14.38 skrev Steven Neumann:
>
> Dear Gromacs Users,
>
> Is there any way in Gromacs which will allow me to contraint some of the
> atoms in the system to move only in the coordinate X and Z? I do not want
> some of my atoms to move in Y direction. Do you know how to do this?
>
>
> Hi,
>
> Not exactly. But you can apply position restraints with zero force constants
>  in X and Z directions. This will allow some movement in the Y direction,
> but the extent depends on your force constant in the Y direction.
>
> Erik
>
> Steven
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> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
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>
>