[gmx-users] minimization -- bugzilla or general advice?

David Mobley dmobley at gmail.com
Thu Mar 27 20:59:06 CET 2008


> I assume you are using a rigid water model, and thus constraints via SETTLE.

Yes, OK.

> Constraining is required to measure the size of the force (for convergence
> and
> step size adjustment) and to make correct steps without enormous extra
> displacements in the direction of the force which could cause problems due
> to non-linearity.
> In Gromacs 3 we had only a coordinate version of SETTLE and LINCS
> did not work well for "triangle constraints". So to constrain the force
> during EM
> we needed to use only coordinates. The trick is to add c*f to the
> coordinates,
> somewhat analogous to constraining velocities in leap frog, and then get the
> force without constraint components as:
> (x+c*f - constrained(x+c*f))/c
> I chose c as the minimization step size divided by the maximum force.
> But there are two issues here, for large c non-linearity problems
> and for small c float/double accuracy issues.
> The non-linearity issue could be causing your problems.

> Although there is also another issue: water is difficult to minimize in
> general.

Hmm. Is this different from how other packages handle this issue? I
have never had the recurring problems with minimization in GROMACS
that I have in other packages. Even though, strangely enough, water is
a common feature in most of the simulations I run.

I'll try and give this a shot in GROMACS 4 soon, I suppose. And I'll
put together a bugzilla.


> Berk.
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