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

Grace Li fullofgrace88 at gmail.com
Wed Mar 5 23:16:23 CET 2008

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?

Specifically, I have used the following:

1. I have tried using bonds type 6 in my topology:
[ bonds ]
;  ai    aj funct c0 c1 c2 c3
   9   413     6 8.18  421.54

2. When using distance restraints, I added the following lines to my
topology file:
[ distance_restraints ]
;ai     aj      type    index   type   low     up1     up2     fac
 9     413    1         0         1       8.18     8.18      10.0

In the case of using [ distance_restraints ] in the topology file, I
added the following lines to my .mdp file:
disre = simple
disre_fc = 421.54
disre_weighting = equal
disre_tau = 0
(and various other values of the force constant, disre_fc, but in all
cases the run crashes).

Thanks for any suggestions!

More information about the gromacs.org_gmx-users mailing list