[gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error

João M. Damas jmdamas at itqb.unl.pt
Fri Oct 9 18:17:47 CEST 2009

What do you mean by mutually inconsistent? From what I understand, they

Also, [bonds] type 6 won't work for what I want, since I don't want to keep
the molecules at a fixed distance but to prevent them from coming closer,
i.e. I want a potential that depends on the distance between the atoms.

Testing the distance restraints can be quite exhaustive when you have about
160 restraints, and I am considering just the test case I'm trying, not the
actual system which will have some more organic molecules, which will lead
to a greater amount of combination of restraints...


On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> João M. Damas wrote:
>> Gromacs users,
>> I have a small test system of about 2500 atoms which consists on a few
>> organic molecules in a box of water. I'm trying to use distance restraints
>> to keep each molecule apart from each other and I've failed until now.
>> I'll start by saying that the simulation runs smoothly without using
>> distance restraints and that I've created a single molecule topology that
>> describes all organic molecules, allowing the use of distance restraints. By
>> applying just one distance restraint between two atoms of different
>> molecules, the simulation still runs without problems. When I apply all the
>> distance restraints I want, the system crashes in the first few steps with
>> an XTC error, which is preceded by a few inconsistent shifts and some LINCS
>> warnings. Varying the number of restraints that I use, makes the crash
>> happen at later steps (500ish), meanwhile giving a lot of inconsistent
>> shifts before crashing with a fatal error: Number of grid cells is zero. I
>> know it seems I'm experimenting blindly, but varying the number of
>> restraints was the first that occurred to me.
>> I've searched the list for similar problems and tried a few more tests.
>> I've turned off LINCS and reduced the time step and it didn't solve the
>> problem, the box blew up after a few steps due to pressure problems. Since
>> it could be a PBC problem, I tried to increase the size of the box, but it
>> didn't solve the problem. Turning of PBC did solve the problem, but I really
>> need PBC. I've also changed the low, up1 and up2 to values inferior to half
>> the box size (I don't even care about the up1 and up2 values in this
>> application, and I was setting them to 5.0 nm before), but it didn't solve
>> the problem either. I'm a little on a dead end here and I was hoping anyone
>> could give me some insight.
>> By the way, I'm using GROMACS 4.
> The simplest explanation is that your sets of distance restraints are
> mutually inconsistent. This destabilizes the system and eventually leads to
> your symptoms. Consider using [bonds] type 6, per advice of manual section
> 4.3.4. Either way, if you add these restraints one by one after testing that
> the previous set seemed to work OK (didn't crash, trajectory looks right),
> you may uncover your issue.
> Mark
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
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