[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:
> 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
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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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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