[gmx-users] Stepsize too small.

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 9 10:24:01 CEST 2003

On Tue, 2003-07-08 at 18:32, Joel DeWitt wrote:
> gmx-users:
> I've decided to backtrack and test-run EM on a system utilizing the original
> PDB file used to construct the monolayer mentioned in my last post.  The
> system is a DPPC bilayer composed of 64 lipid molecules and 3846 waters.
> Now, when I try to run EM, no matter what parameters I choose in "em.mdp," I
> keep getting the following error message (i.e. the simulation bombs):
> Stepsize too small (... nm)Converged to machine precision,
> but not to the requested precision (...)
> Any suggestions on choosing values for "emtol," "emstep" and the number of
> steps?
the steepest descent algorithm is rather shitty. congrad might give you
better results if you compile in double precision.

If your only aim is to start a MD simulation then it steep is good
enough and you can use the final conformation from the minimization as
input for the MD sim.

> Joel DeWitt
> Department of Physics
> Oklahoma State University
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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://xray.bmc.uu.se/~spoel

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