[gmx-users] Constraint causing system to explode

[chris.neale at utoronto.ca]

Dear Warren:

I don't have your answer, but I'll point out that when you ask: "Is it  
possible that this is a problem that arises because of domain  
decomposition over multiple nodes" that you are probably the person in  
the best position to address this. 300ps should not take too long to  
simulate so why not try it on a single node and also on multiple nodes  
with mdrun -pd and report back?

Somebody may have your answer, but the system blowing up question is  
so common that it is probably faster for you to rule out some things  
first.

Chris.

-- original message --

	I am looking at the the free energy profile of end-to end distances  
of various peptides, but I am consistently getting a system blow-up  
when running simulations with that distance constrained by a type 2  
constraint.

	I run a simulation of the unconstrained peptide in a box of tip4p  
water, Na+ and Cl- ions, and it runs with no problem.

	Then I grab a frame of that simulation in which the end-to-end  
distance is 0.8 nm (full frame including water) as a .gro file.  Then  
I add a type 2 constraint between the N-terminal nitrogen atom and the  
C-terminal carboxyl carbon, create a new .tpr file using the revised  
topology and the already equilibrated frame as starting files and a  
.mdp file that now has the free_energy set to on, and then launch mdrun.

	About 189 ps into the simulation I start getting warnings as follows,  
ultimately leading to blow-up and the run failing (fragment of error  
file output shown at end of message).

	I am obviously missing something about how the constraint is handled.  
  Is it possible that this is a problem that arises because of domain  
decomposition over multiple nodes, ir is there something more basic  
that needs to be dealt with when imposing a type 2 constraint?

Warren Gallin

Step 94636, time 189.272 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.041028, max 0.161215 (between atoms 217 and 219)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length

Step 94637, time 189.274 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018884, max 0.100333 (between atoms 217 and 218)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length

<SNIP>