[gmx-users] Problem with using distance restraints (disre) with PBC
Mitchell Stanton-Cook
s4026869 at student.uq.edu.au
Thu Mar 6 03:50:18 CET 2008
Hi Tom,
Have you modified the src? As far as I know this has not been done in
331 or 332. I'm unsure of 333. I would be interested in the patch. As
far as I know the problem is due to the the distance/orientation
restraints being placed in the bonded graph. There was a bit of chatter
on the developers list in 2007 about this but I haven't heard much else.
For my system I was using a truncated dodecahedron box. The box vector
1/2d was my biggest problem. I simply changed to a triclinic box without
too much cost. However I think I could grab an extra 300ps/day if I had
an actual fix.
Cheers
Mitch
TJ Piggot wrote:
> 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.
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
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