[gmx-users] Numerical Stability of Gromacs Implementation

[Justin Lemkul]

On 8/13/14, 2:19 PM, Johnny Lu wrote:
> Hi again.
>
> Some of my friends said that gromacs had lower numerical stability than
> amber, and occasionally has mysterious error in energy.
>

I have never seen convincing evidence to support such a claim.  Some people have 
stated that they have found evidence of problems, but those claims (at least the 
recent ones that I have seen) have been debunked.

> Is that still true? Does the implementation of Integrator cause more
> resonance effect?
> 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.)
>
> Why do people still use and paid for amber, when gromacs is free?

One reason is that AMBER has many features that Gromacs does not.  Another 
reason might just be tradition; some labs get set in the way they do things and 
don't change.

> 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.
>

Usually you only need one MD engine.  AMBER has also been around for 
considerably longer than Gromacs.  I see more papers that use Gromacs and NAMD 
than anything else, these days.  But that could be just based on what I read :)

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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