[gmx-users] a problem with a DNA simulation using the g53a6 forcefield

[Kristina Nicole Woods]

Hello all:

I am trying to do a simulation of a short fragment of double stranded DNA
(12 base pairs) using the g53a6 forcefield.  But during the minimization
step the DNA is pulled apart and I'm not sure what I am doing wrong.  Here
is the .mdp file for the minimization step that I have tried using:

---------------------------------------------------------------------
;       Wed Nov  3 17:12:44 1993
;       Input file
;
cpp                 = c:/Progra~1/gromacs/bin/cpp
include             =  -I/cygdrive/c/DNA_normal/gromacs_dna/53a6
-I/cygdrive/c/Progra~1/gromacs/share/top
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  100
;
;       Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01

coulombtype         = PME
rvdw                = 1.4
rlist               = 0.8
rcoulomb            = 1.4
fourierspacing      = 0.12
pme_order           = 4
ewald_rtol          = 1e-5

vdwtype             = cut-off
pbc                 = xyz
ns_type             = simple
dispcorr            = enerpres
---------------------------------------------------------------------

I was wondering if anyone can point out any serious problems that I have
that would cause this to happen?

I should also mention that the fragment of DNA is contained within a box
with dimensions of 3.71 nm/3.38 nm/4.30 nm and solvated with a 0.25 nm
shell of water.

Any help would be greatly appreciated!

Kristina :)