[gmx-users] Numerical Stability of Gromacs Implementation

[Mark Abraham]

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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