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.
/Erik
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
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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