[gmx-users] DFLEXIBLE parameter

Berk Hess gmx3 at hotmail.com
Fri Oct 31 10:56:20 CET 2008


The simple answer is: NEVER EVER do simulation with -DFLEXIBLE for water.
The results will be nonsense, as the standard water models have only been parametrized
with rigid bonds and angles.

The only use for this option used to be energy minimization.
But as of Gromacs 4.0, all minimizers work with constraints,
so now you really never need -DFLEXIBLE.


> Date: Fri, 31 Oct 2008 00:26:30 -0400
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] DFLEXIBLE parameter
> define = -DFLEXIBLE will affect your run most definitely. Exactly how  
> it will affect your run is, to my knowledge, not yet published. The  
> common assumption is that it does not matter at all when you are  
> interested in the solute, which most of us are. To include this  
> parameter is to allow the O-H bond in many water models to vibrate, as  
> opposed to being constrained to a constant equilibrium distance.  
> However, most users desire a computationally faster run utilizing  
> constraints = all-bonds and a timestep of 2 fs, or constraints =  
> h-bonds and a timestep of 1 fs, versus constraints = none and define =  
> -DFLEXIBLE that requires a timestep of 0.5 fs.
> Note that it does not appear to affect all water models (e.g. tip5p)
> The 4.0 manual makes an interesting argument that all bond vibrations  
> are very much quantum characteristics and are thus equally well  
> represented by a constraint as they are by a harmonic restraint.
> That's a rambling response, I know, but you need to focus your  
> question more tightly or include more relevant information if you want  
> something more direct for an answer.
> Chris.
> -- original message --
> Dear all gmx users and developers,
> Parameter -DFLEXIBLE in mdp file will include flexible water in stead  
> of rigid water into the topology.
>   So, will it affect the MD simulation if I include this parameter in  
> the MD simulation? because it is unnecessary in the run parameter.
> Any comments and suggestions will be well appreciated.
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