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

[Mitchell Stanton-Cook]

I have had a similar problem with orientation restraints.

Are the residues far is space? Are you getting inconsistent shifts? If so -

If so re-define your box size so that the shortest box vector is greater 
than the distance restraint residue + some tolerance.

I also noticed -

[ distance_restraints ]
;ai     aj      type    index   type   low     up1     up2     fac
 9     413       1         0     1       8.18     8.18      10.0
 1.0

Have you defined the low up and up2 in the correct units?

Cheers

Mitch

TJ Piggot wrote:
> Hi,
>
> 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
>
> Cheers
>
> Tom
>
> --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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