[gmx-users] freezing/position restraints and minimization

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 17 14:13:25 CET 2007

Jeroen van Bemmelen wrote:
> Hmm, interesting...
> And what about the -DFLEXIBLE definition in your mdp file during 
> steepest descent minimization? Do you know if that will also deform 
> your (SPC) water molecules? And will that deformation be corrected 
> again during the first equilibration step(s)?
> I ask this, because I read on severel places (e.g. the online mdp 
> options manual and in one of the tutorials) that you could use the -
> DFLEXIBLE definition to "allow steepest descent to minimize further". 
> So I've used it for most of my minimizations up til now, assuming 
> that was the right thing to do.
it is fine, but your bond lengths and bond angle in water will be 
slightly off the equilibrium values. This will be corrected during th 

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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