[gmx-users] Fwd: Warning: 1-4 interaction

Joern Lenz JLenz at zbh.uni-hamburg.de
Thu Apr 12 16:56:38 CEST 2007

sorry, but i forgot to say that the distance between this tyrosine and the P 
of the DNA was from a previously calculated MD simulation.
when i tried to add the following line into the (see below) mdp file:
table-extension = 2
the warning messages becomes 

Warning: 1-4 interaction between 8159 and 8184 at distance 2.017 which is 
larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,

these atoms correspond to the interesting P of my DNA and C4' of the previous 
nucleotide in the DNA
any suggestions ?
thanks very lot

----------  Forwarded Message  ----------

Subject: Warning: 1-4 interaction
Date: Thursday 12 April 2007 16:35
From: Joern Lenz <JLenz at zbh.uni-hamburg.de>
To: gmx-users at gromacs.org

dear gromacs guys,
i have the following problem:

i linked the phosphate atom of a DNA to the phenolic-hydroxyl group of a
proteins tyrosine by defining a line in the specbond.dat file.
the distance before linking these atoms was about 4.2 angstroms.
my intention now was first to minimize the linked complex using the following
mdp file:

integrator      = steep
dt              = 0.002
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      = 0.0005

starting the minimzation the following warning occurs - and i know that this
problem was discussed often before :

Warning: 1-4 interaction between 1435 and 8183 at distance 1.862 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

i know what this error message means.  Their 1-4 distance is too long.
the mentioned atoms are of the DNA and the tyrosine respectively.
my question now is: how can i fix this warning ? since i run minimzation and
this warning occurs i do not know exactly how to go on becuase i run
minimization in order to shrink the bond-length between protein and dna.
how else can i shrink it to avoid the warning ?
does anyone has an idea that would help me to gon on with my work ?
thanks a lot in advance and have a nice spring-day evening


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