[gmx-users] Warning: 1-4 interaction
JLenz at zbh.uni-hamburg.de
Thu Apr 12 16:35:06 CEST 2007
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
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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