[gmx-users] DFLEXIBLE parameter

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Oct 31 05:26:30 CET 2008

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.


-- 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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