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

[D. Flemming Hansen]

Hi,

I am sure what exactly you are trying to simulate, but your distances 
seem a bit large (8.1 nm) for a small peptide. Having your restraints 
_far_ off may cause a crash.

Flemming


On 5 Mar 2008, at 17:16, 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?
>
> 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
>  1.0
>
> In the case of using [ distance_restraints ] in the topology file, I
>  have
> 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!
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