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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