[gmx-users] Question about DNA simulation

[bo yang]

Hi,
When I do the DNA MD simulation. I use pdb2gmx, and the water model I used
is spc.gro.
I did the editconf and genbox. The following is my em.mdp file.
------------------------------------------------------------------------------------------------
define          =-DEFLEXIBLE
integrator      = steep
;gen-vel         = yes
;pbc             = no
;comm_mode       = angular
nsteps          = 2000
epsilon_rf       = 82
nstlist         = 100
ns_type         = grid
rlist           = 1.3
dt              = 0.0005
tc-grps         = system
tcoupl          = Berendsen
;freezegrps      = CNT
;freezedim       = N
tau-t           = 0.1
temp            = 450
ref-t           = 450
;pcoupl          = Parrinello-Rahman
;pcoupltype      = isotropic
;tau-p           = 0.5
;ref_p           = 1.01325
;compressibility = 4.5e-5
coulombtype     = pme
rcoulomb        = 1.3
vdw-type        = cut-off
rvdw            = 1.3
nstenergy       = 10
optimize_fft    = yes
emstep          = 0.2
emtol           = 100
constraints = none
-------------------------------------------------------------------------------------
Q1, I am not sure whether should I put the "define  = -DFLEXIBLE" in the
em.mdp.
Q2,
When I perform the preprocess for energy minimization (grompp), the error
message is :
"Fatal error:
[file "/home/nano/gromacs/share/gromacs/top/spc.itp", line 41]:
             Atom index(1) in setttles out of bounds (1-0)"

I looked back to the spc.itp, from line 39 to 41:
----------------------------------------------------------------------
[ settles ]
; OW    funct    doh    dhh
1    1    0.1    0.16330
---------------------------------------------------------------------
Can you give me any suggestions about how to correct it and why?

Best regards!
Bo
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