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

Berk Hess gmx3 at hotmail.com
Fri Mar 28 10:22:52 CET 2008

> Date: Thu, 27 Mar 2008 12:59:06 -0700
> From: dmobley at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] minimization -- bugzilla or general advice?
> Berk,
> > 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.
> Thanks,
> David

I would guess other packages would use a RATTLE like constraint algorithm,
both for water and other molecules.
So this could be the source of the problem.
But please try 4.0 before submitting a bugzilla and speculating further.


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