Chris,
As you suggested, I ran it on one node, and it still blew up, so it
appears to be some oddity with the constraint that I am imposing.
When I look at the dgdl.xvg file from the run, there appear to be a
number of transient spikes that are a couple orders of magnitude larger than
the typical variation during the run, and I am getting errors on an angle
changing by more than 30 degrees as a LINCS warning during those short spikes.
The final system blow-up starts with the same situtation, which degenerates
into a full blow system explosion, with bond lengths going to crzy high values.
So my question boils down to this: What is it about a type 2
constraint that will generate these ridiculously large forces on relatively
rare occasions? Or perhaps, what error am I making in setting up the
simulation that would cause only the constrained system to manifest this
behavior?
Warren Gallin
On 2010-05-27, at 11:22 AM, chris.ne...@utoronto.ca wrote:
> 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>
>
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