[gmx-users] Energy Minimization with Lipid Bilayer

[Tsjerk Wassenaar]

Hi Justin,

My guess is that you've generated severe overlaps. On your starting
structure (the one you use as input to grompp) run trjconv -s in.gro
-f in.gro -o out.pdb -pbc inbox
That will map all your atoms to the basic simulation cell. You should
visually inspect the output using your favourite viewer. You're likely
to see all kinds of bonds in the solvent which shouldn't be there,
indicating that you have overlapping residues.

> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  5.9484382e+18
> Maximum force     =            inf on atom 6417
> Norm of force     =            nan

This is soooo bad. The potential energy should be negative, rather
than around 6000000000000000000 :)

Cheers,

Tsjerk

On 11/22/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Justin Lemkul wrote:
> > Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
> >
> >
> >>Justin Lemkul wrote:
> >>
> >>
> >>>I also tried running a position-restrained MD (just to see if it might give
> >>
> >>me
> >>
> >>>something different), holding the DPPC bilayer fixed and allowing the
> >>
> >>solvent
> >>
> >>>to move, but I was again frustrated to see:
> >>>
> >>>Warning: Only triclinic boxes with the first vector parallel to the x-axis
> >>
> >>and
> >>
> >>>the second vector in the xy-plane are supported.
> >>>         Box (3x3):
> >>>            Box[    0]={         nan,          nan,          nan}
> >>>            Box[    1]={         nan,          nan,          nan}
> >>>            Box[    2]={         nan,          nan,          nan}
> >>>         Can not fix pbc.
> >>>
> >>>In the MD, I am applying PBC.  I am wondering if this output is a result of
> >>
> >>a
> >>
> >>>poorly minimized starting structure, or if these errors are in any way
> >>
> >>related?
> >>
> >>Hmmm in order that we can see what your .gro file is doing, can you
> >>please post the results of
> >>
> >>head -n 10 conf.gro
> >>tail -n 10 conf.gro
> >>wc -l conf.gro
> >
> >
> > Hopefully this will help:
>
> Unfortunately all seems to be in order there. The second line has the
> right number of atoms for the number of lines in the file, and the box
> in the final row has the right format.
>
> Can you mail me your .gro, .mdp and .top (and appropriate #included .itp
> files) off-list and I'll take a look?
>
> Mark
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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