[gmx-users] infinitive force acting on atom during

Joern Lenz JLenz at zbh.uni-hamburg.de
Mon Jan 15 12:33:08 CET 2007

Dear Tsjerk, dear gromacs-users and developers,
thank you for your kind help and information about my problem.

However, the atom  "atom 2005" (see below) which feels an infinitive force 
acting on it is a water molecule which is not in the original pdb file which 
I used for my simulations. 
So I guess if I (although I have not tried it yet) do the simulation in vacuo 
this problem might not occur because this water molecule is absent then. And 
the system without water molecules consists of a 17bp dsDNA docked into a 
protein. I have 24 protein DNA complexes like this. Two of them show the 
described problems, the rest is fine. So I cannot see how to solve this 
Have you or anyone else got an idea of what goes wrong in my simulation?
And another thing is (perhaps a stupid question ?!?): why is it better not to 
use a cubic box for the simulation ?
Thanks a lot for your help and guidance.


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*).



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

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