[gmx-users] freezing/position restraints and minimization
Jeroen van Bemmelen
J.J.M.vanBemmelen at tnw.tudelft.nl
Sat Mar 17 12:50:04 CET 2007
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.
On 17 Mar 2007 at 12:00, David Mobley wrote:
> Sorry to e-mail so much. But it seems this is, indeed, the problem.
> For freeze groups to work in minimization you need to use a minimizer
> which is can handle constraints properly. In GROMACS the only
> minimizer that is set up to handle constraints properly is steepest
> Note that this also has implications for anyone using rigid water
> models (most of us): If you're "minimizing" with L-BFGS or other
> minimizers aside from steepest descents, you're probably deforming
> your water molecules, as well.
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