[gmx-users] infinitive force acting on atom during minimization

[Tsjerk Wassenaar]

Hi Joern,

Did you first perform an energy minimization in vacuum? The values you
get indicate severe problems with your starting structure.

By the way, for such a system you don't want to use a cubic box. It's
an utter waste of resources. You're better off with a rhombic
dodecahedron, or you can contact me off list if you want to cut your
volume by half and still have the same distance between periodic
images (right, speed up your simulations >2*).

Cheers,

Tsjerk

On 1/12/07, Joern Lenz <JLenz at zbh.uni-hamburg.de> wrote:
> dear users,
> i try to simulate a system of DNA (17 bp) and a protein (420 aa).
>
> before i start my MD runs, i solvated the system in a cubic box (-d = 0.9) and
> started a minimization of it using the em.mdp file which you can see at the
> bottom of this email.
> unfortunately the minimization breaks (see below).
> And if it does not break, it is very slow (20 iterations take about 3 weeks).
> Can you see from the information i give to you, why this happens?
> The output of this minimizations looks something like:
>
> Steepest Descents:
> Tolerance (Fmax)   =  1.00000e+00
> Number of steps    =          400
> Step=    0, Dmax= 5.0e-04 nm, Epot=  4.14463e+16 Fmax=  inf, atom= 2005
> Step=    1, Dmax= 5.0e-04 nm, Epot= nan Fmax= 0.00000e+00, atom= 0
> Step=    2, Dmax= 2.5e-04 nm, Epot= nan Fmax= 0.00000e+00, atom= 0
> Step=    3, Dmax= 1.3e-04 nm, Epot= nan Fmax= 0.00000e+00, atom= 0
> Step=    4, Dmax= 6.3e-05 nm, Epot= nan Fmax= 0.00000e+00, atom= 0
> ...
>
> Hence there is an infinitive force acting on atom 2005 in my system, right ?
> First I looked at the coresponding file to figure ot which residue this atom
> belongs to. I then looked at the system using chimera as a viewer and found
> that is residue occurs several times in my system, which worries me a little
> bit. But there is no such thing like two atoms lying very close to each other
> which would explain the Fmax=  inf, atom= 2005 line in the minimization.
> Has anyone got an idea of what is going wrong here or do you need more
> information about my used files.
>
> It would be of great help for my further work, so thanks a lot in advance and
> have a nice weekend
> Greetings
>
> ====================
> em.mdp:
>
> title                   = Minimization of blah.pdb
> cpp             = /usr/bin/cpp
> define          = -DFLEX_SPC
> integrator      = steep
> nsteps          = 400
> nstenergy       = 5
> nstxtcout       = 5
> nstlist         = 5
> ns_type                 = simple
> rlist                   = 1.0
> coulombtype     = PME
> rcoulomb        = 1.0
> rvdw            = 1.0
> pbc                     = xyz
> fourierspacing  = 0.12
> fourier_nx      = 0
> fourier_ny      = 0
> fourier_nz      = 0
> pme_order       = 4
> ewald_rtol      = 1e-5
> optimize_fft    = yes
> constraints     = none
> emtol           = 1.0
> emstep          = 0.005
> ====================
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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