erikm at xray.bmc.uu.se
Wed May 2 14:08:24 CEST 2007
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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