tsjerkw at gmail.com
Wed May 2 15:47:45 CEST 2007
Also look at the energies. If Erik's local energy minimum is indeed an
all-time energy maximum (infinite energies, infinite forces), you're
starting structure is indeed your worry. But then again, if you
started from an energy minimized membrane, there's not much to
minimize anymore. Now, we can't tell either way from the information
On 5/2/07, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 2 maj 2007 kl. 13.41 skrev Sona Aramyan:
> > Hi everybody
> > I'm trying to do em with l-bfgs integrator but it
> > finishes with 0 steps.
> > My system is 128dppc and 30 per lipid water.
> > when I'm using steep integrator it converged to
> > machine precision say 15 steps.
> > What I'm suggesting is that my system has very bad
> > starting configuration and maybe it is in somekind of
> > local minimum, and because my Gromacs is in single
> > precision it can't get out of that minimum.
> A local minimum is a local minimum, regardless of precision. The
> minimization will not jump across any ridges in the energy landscape.
> > Now I'm running 64dppc bilayer without water for 1ns
> > and then I'm going to duplicate it, to minimize the
> > result and then solvate.
> > Am I right????
> > Any suggestions will be very appreciated.
> > Beforehand THANK YOU
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> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 4537 fax: +46 18 511 755
> erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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