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

[TJ Piggot]

I agree with increasing the size of the box (if seeing inconsistent shifts, 
as i should have mentioned in my previous post) and in this case it is 
practical to do as the system is quite small. However (just for future 
reference) if the problem were in a much larger system (as it is in my 
case) then it may be more suitable to modify the source code to avoid 
increasing the size of the system simulated.

Tom

--On Thursday, March 06, 2008 11:52:01 +1000 Mitchell Stanton-Cook 
<s4026869 at student.uq.edu.au> wrote:

> 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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>
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.