[gmx-users] l-bfgs

[Tsjerk Wassenaar]

Hi Sona,

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
you give...

Tsjerk

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.
>
> /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
> >
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam protection around
> > http://mail.yahoo.com
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> _______________________________________________
> 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
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623