[gmx-users] PBC, lincs and bonds breaking

[Mark Abraham]

> I am trying to simulate my own structure based simulation using 3.3.2.

What sort of structure?

> I
> 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
> will
> cross the boundary and that single atom will get placed on the opposite
> side
> 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
> lincs,
> 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 :-)
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation

> 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?

Mark