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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