Dear Users !
I have done a minimization for a tetrapeptide in a water box
with conjugate gradient minimization of 1000 steps
when I convert it to pdb as below
------------
trjconv -f em.trr -o min.pdb -s em.tpr << EOF
0
EOF
--------------------
the out put pdb has many structures
as follows
MODEL 0
MODEL 1
MODEL 2
but the minimized pdb is single structre ,
what does these structures mean.
how to obtain a single structre.
my mimization input file is as follows
--------------------------------------
define = -DFLEXIBLE
constraints = none
integrator = cg
dt = 0.001 ; ps !
nsteps = 1000
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 10.0
emstep = 0.01
energygrps = protein SOL
----------------------------------------
thanks in advance
--
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