[gmx-users] Numerical Stability of Gromacs Implementation

[Johnny Lu]

Sorry for asking this. Is it possible for me to get some references about
the claims of instability of gromacs simulations, and their debunk?

>From the few papers that I read, I guess algorithms of molecular dynamics
do not treat all observables equally well.
Some old papers say that the velocity in velocity verlet is not symplectic,
but rather follows some shadow hamiltonian or generalized equipartition
theorem.
Then another one mentioned force splitting can reduce the resonance effect
caused by integrator.
That said, very few papers talk about this.

I don't know much about the effect of MD on the observables that I try to
look at.
And, sorry for replying this late, I have been installing gromacs on aix
for a week.
Compiling gcc took 3 days of computer time.


On Thu, Aug 14, 2014 at 2:29 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Wed, Aug 13, 2014 at 1:19 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > Hi again.
> >
> > Some of my friends said that gromacs had lower numerical stability than
> > amber, and occasionally has mysterious error in energy.
> >
>
> Show us a result and we'll discuss fixing it ;-)
>
>
> > Is that still true? Does the implementation of Integrator cause more
> > resonance effect?
> >
>
> Any numerical software can be used poorly. Any numerical software can have
> bugs. Give them the same input to two implementations of the same algorithm
> and they should give results that are similar (whatever that means in the
> problem domain).
>
>
> > I am trying to run NVE simulation with the single precision version, and
> so
> > I guess the implementation of thermostats is not my most immediate
> concern
> > at the moment.
> >
> > I searched online, and haven't found much about numerical instability of
> > gromacs using amber forcefield (I mean for version 4.6, which supports
> the
> > amber force-fields without modification.)
> >
>
> What do you mean by numerical stability? Should you actually be concerned
> about getting a correct physical observable? People look at energy
> conservation because it is easy to do, but connecting that to the quality
> of the resulting physics is non-trivial. Even if you can (say) deliver
> state-of-the-art energy conservation (and most packages can do this in some
> mode), you still need to measure the price in simulation throughput
> incurred by running in that mode. The overall objective is to deliver
> science of sufficient quality with minimal time to solution. In some cases,
> it is right to let some energy leak and let the thermostat fix it, if you
> generate many more samples by so doing.
>
> Why do people still use and paid for amber, when gromacs is free?
> > I look online and the number of papers that use amber is about twice of
> the
> > number of paper that use gromacs. There are very few papers that
> mentioned
> > both gromacs and amber.
> >
>
> Inertia is a big effect. You tend to adopt the package used by the local MD
> expert so you have a low-latency person of whom to ask questions. They tend
> to still use the package they used in their doctoral work, regardless of
> current technical merit, because learning to use such software well is
> tricky and discarding your old workflows is not a cheap proposition. The
> next biggest effect is what functionality is available, and at what
> performance.
>
> Mark
>
> Thank you.
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