[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 01:40:51 CEST 2009

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.

Thanks in advance and sorry if I sounded confusing.

Best regards,
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
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