[gmx-users] distance constrain

[Luciane V. Mello]

Hi Uwe

Thanks for the pointer, but actually I want a simple harmonic potential
rather than the more NOE-orientated distance restraints.

>From page 91 of the manual 3.1, it looks as if I need a bond type 6
definition.  How can I add one to my topol.top file?  Where to define
the parameters rij and kij (Fig 4.5)?

Thanks in advance

Luciane

> Hi Luciane,
> 
> this is an easy thing to do. You need a section [ distance_restraints ] 
> in you topology
> or itp file. The format is described in chapter 4.2 of the manual (for 
> gromacs 3.1).
> Note that you cannot define distance restraints between atoms in 
> different molecules, so
> if you want to do something like this, you need to define the two 
> molecules within one
> molecule section.
> 
> Regards,
> Uwe
> 
> Luciane V. Mello wrote:
> 
> >Dear all,
> >
> >
> >How would you constrain the distance between two atoms during the
> >simulation?
> >I've looked at genpr, but it fixes the atoms rather than restrains their
> >distances.
> >
> >Thanks in advance,
> >
> >Luciane
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> 
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