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

TJ Piggot t.piggot at bristol.ac.uk
Thu Mar 6 02:42:56 CET 2008


Firstly I would strongly reiterate what Mark said. I would make sure the 
distance restraints are causing your problem. Again as Mark said make sure 
you can simulate your system without the distance restraints, and then I 
would try to simulate the system with distance restraints and with a much 
larger box of water surrounding your peptide. Here you should also be able 
to overcome the problem (if it is this problem) with a large enough 
distance between periodic images.

If you can then confirm what you have suspected to be the problem you will 
need to modify the source code slightly. If you search the list (searching 
for "inconsistent shifts using multiple bonds type 6") you can see the 
changes you need to make, as suggested by Berk Hess to me when i had this 
problem with bond type 6.

Hope this helps



--On Wednesday, March 05, 2008 17:16:23 -0500 Grace Li 
<fullofgrace88 at gmail.com> 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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TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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