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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 9 01:51:47 CEST 2009

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.


More information about the gromacs.org_gmx-users mailing list