[gmx-users] how to get a minimized structure pdb

[balaji nagarajan]

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 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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