[gmx-users] l-bfgs

[Sona Aramyan]

Thanks very much for you advises.
Actually I just made one molecule of dppc using
information from leterature about its bond lenghts and
angles and so on... and then run md with that one
molecule and then multipled it. First I made 16 dppc
bilayer with 480 water and then from that 16dppc I
made 32 and then 64 and now I have 128dppc.
Every time I was running that bilayers like for 2 or 5
ps and then duplicated them.
My ultimate aim is to made 2048 dppc bilayer.

Sona

--- Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
> > >
> > >
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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
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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