[gmx-users] Constraint causing system to explode

[Mark Abraham]

----- Original Message -----
From: Warren Gallin <wgallin at ualberta.ca>
Date: Tuesday, June 1, 2010 13:38
Subject: Re: [gmx-users] Constraint causing system to explode
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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.

Does it happen with a distance restraint, instead? (Is that a better physical model?) Is there any possible correlation with one atom crossing a PBC boundary, such that a buggy implementation would then be horribly broken on the next step?

Mark

> 	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.neale at 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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