[gmx-developers] Reaction Filed crash!

baptista at itqb.unl.pt baptista at itqb.unl.pt
Sun Dec 18 01:27:42 CET 2011

On Sat, 17 Dec 2011, Berk Hess wrote:

> I will try to clarify the situation a bit.
> Pre-4.5 there were 4 approximation/errors in this typical "Gromos" setup
> and a complicating factor:
> 1. Non-buffered pair-lists reused for nstlist-1 steps: no real Hamiltonian
> 2. Reaction-field with epsilon_rf<infinity: discontinuous energy and force at 
> cut-off
> 3. Twin-range interactions (or multiple time stepping) with 5*2=10 fs for the 
> forces
> beyond 0.9 nm, but the reorientation of water only allows time steps up to 5 
> fs
> 4. A non-reversible multiple time stepping scheme
> 5. A thermostat with strong coupling (pre-4.0 also Berendsen: one other 
> error)
> Factors 1-4 cause serious integration errors in the long-range electrostatics
> which all lead to serious heating of the system, but different for water and 
> protein.
> Factor 5 couples off this heat, but with such strong heating you no longer 
> know
> what happening.
> In version 4.5 I fixed factor 4. This takes out one source of error and 
> heating.
> But as different errors affect different aspects/components differently, it's 
> very
> difficult to tell what will happen.
> Factors 1-3 can be fixed at a high computational cost (although 4.6 might 
> help here).
> My hypothesis is that factor 4 caused massive heating everywhere and combined
> with a strongly coupled thermostat, all effects a seriously dampened, 
> including those of 1-3.
> Fixing factor 4 gives less heating, thus less thermostat coupling and 
> possibly less
> uniform heating between water and protein (due to effects of 1-3 being damped 
> less),
> causing hydrogens in the protein to overheat. But as there are so many 
> complicating factors,
> it's difficult to find out what's really happening.
> When I fixed factors 1-3, by different mdp settings, I get perfect energy 
> conservation in 4.5,
> but that's at a high computational cost.
> Cheers,
> Berk

Thanks for clarifying the different factors involved. I see what you mean. 
The relation between these factors is intricate and difficult to 
antecipate, and trying to fix one of them ended up making things unstable 
when using some setups (such as ours).

You mention that 4.6 might help with factors 1-3. Does that mean that
you are making further changes? Assuming that we decide to stick with
our current setup, would you then advise us to stay with 4.0 for now
and wait for 4.6 to be released?


> On 12/17/11 22:12 , Shirts, Michael (mrs5pt) wrote:
>> A couple thoughts:
>> 1. if something was stable before (even if it was not best practices), then
>> I agree that it should be stable in the current code, unless the previous
>> algorithm was wrong to begin with.  I haven't looked into the details best
>> to know what the problem is yet.
>> 2. Massive heating damped with temperature control will drive you away from
>> an equilibrium to a steady state where some properties become incorrect 
>> even
>> if others are correct.  So you do have to be very careful that the
>> properties you looked at before are the same ones.  Where exactly the
>> failure point is is very hard to say very clear information about the
>> specific system.
>> 3.
>>> We can also discuss if, as a general rule, using a continuum reaction
>>> field is better or worse than using a lattice method such as PME, but that
>>> is a different issue. Like many other people (Wilfred van Gunsterem, Arieh
>>> Warshel, Alan Mark, Philippe Hünenberger, etc), I'm really not convinced
>>> that lattice methods offer any real advantage, because I find the
>>> published evidences for either their benefits or their artifacs to be
>>> rather weak or contradictory.
>> For HOMOGENEOUS systems, then I agree; the configurations sampled can be
>> achieved by cheaper methods than PME -- basically, the configurations are
>> dominated by short-range effects, and beyond a certain range, all that the
>> extra interactions do is affect the overall energy, which can be calculated
>> pretty well by many methods (including reaction field).
>> When lattice methods are needed is inhomogeneous systems, such as membranes
>> and interfaces, because the long range order affects the configurations
>> sampled, and RF and other continuum methods simply can't handle those well;
>> properties will depend on cutoffs, etc.
>> Best,
>> ~~~~~~~~~~~~
>> Michael Shirts
>> Assistant Professor
>> Department of Chemical Engineering
>> University of Virginia
>> michael.shirts at virginia.edu
>> (434)-243-1821
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