[gmx-users] PBC, lincs and bonds breaking
mark.abraham at anu.edu.au
Sat Oct 27 02:16:41 CEST 2007
> I am trying to simulate my own structure based simulation using 3.3.2.
What sort of structure?
> have developed the forcefield and it works fine without periodic boundary
> conditions. When I use pbc=xyz atoms that are connected in the [bonds]
> section of the topology get broken. What happens is 1 of the two atoms
> cross the boundary and that single atom will get placed on the opposite
> of the box.
This won't be the source of the problem, unless they broke PBC in 3.3.2
and you're the first to notice :-)
> In the next step, the system will explode. If I use lincs, I
> get error messages about angles getting changed and that lincs can not
> satisfy the constraint. I get the same issue with shake. when i run
> the structure is output before the errors and after, so I can see that 1
> atom is placed on the opposite side of the box and that is the same atom
> that I get lincs errors about. Below is my .mdp file.
You don't mention your EM or equilibration regime. Please use one, or
describe yours :-)
> I saw the same errors have been posted when people try to run infinite
> polymers, but I didn't see any resolution to this. Any help would be
> appreciated. thanks
Does the same problem occur for a different part of your system if you
change the seed for generating velocities?
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