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

Berk Hess gmx3 at hotmail.com
Thu Mar 27 13:39:59 CET 2008

> Date: Thu, 27 Mar 2008 07:54:03 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] minimization -- bugzilla or general advice?
> David Mobley wrote:
> > Xavier,
> > 
> >>  I was surprised by the value you use for emstep=1.0e-8. This is the
> >>  "maximum step size" and is in nm! I think that's where your problem is.
> > 
> > I added this recently in testing because I thought perhaps the problem
> > could be due to using too large of steps. It does not help. So
> > everything I send in my previous e-mail holds true regardless of which
> > emstep value I use (default vs 1.0e-8).
> > 
> >>  The minimizer is probably incapable to find anything better for your
> >>  system with this step size and therefore stops.
> >>
> >>  Did you try to keep the default value emstep=0.01 nm or something
> >>  bigger than 1.0e-8?
> > 
> > Also, I think your argument is backwards: steepest descents should
> > work better (but slower) the smaller the step size, I think. If steps
> > are too big it won't be able to move down the gradients accurately
> > enough and risks not being able to find the minimum. The smaller the
> > steps are the more accurately it should be able to find the minimum.
> > 
> David,
> if you add 1+1e-8 in float at least the result is 1. Since coordinates 
> in typical systems are on the order of a few nm such a stepsize does 
> indeed not make sense, but since you tried larger stepsize as well the 
> problem is real. The stepsize is used as the maximum displacement along 
> the force vector in the steep algorithm.
> I encourage you to submit a bugzilla with a few examples.

The problem could be in the constraints.
Gromacs 3 constrains the forces during EM by adding c*f to the coordinates,
constraining those and then dividing the constraint displacement by c.
This limits the accuracy.

In Gromacs 4 I have implemented force constraining for LINCS and SETTLE.
This seems to improve the accuracy a lot.

Could you check if using Gromacs 4 solves your problems?


Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080327/78e8f63e/attachment.html>

More information about the gromacs.org_gmx-users mailing list