[gmx-users] Problem with using distance restraints (disre) with PBC

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 6 00:13:48 CET 2008

Grace Li wrote:
> Hello,
> I am having some trouble using distance restraints. My goal is to apply a
> harmonic potential to the distance between two atoms in a short peptide
> (35 residues). Doing simulations in vacuo, both of the following
> techniques worked to restrain the distance. Also, both techniques worked
> for simulations in water without periodic boundary conditions. As soon
>  as I include pbc = xyz in my .mdp file and use PME for the electrostatics,
>  my simulation crashes (producing step0.pdb and step-1.pdb). I am assuming
> this is because GROMACS is using the distance to the image of the other
> atom, not the actual distance in the box? Is there any way of getting
> around PBC for distance restraints?

Before you assume the distance restraints are the problem, you should 
try the simulation in water and/or vacuum PBC without this interaction.


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