[gmx-users] (no subject)

[minnale]

Hi all, 
I ran protein simulation in water for 9ns and plotted RMSD but it didnt  stabilize, iam doubting on steps what I have done
I am mentioning the steps 

1.EM in vaccum
2.PR in vaccum in NVT
3.EM in water
4.PR in water in NVT
5.Production run for 250 ps in NPT remain 9ns run in MVT condition
6. Intersected the protein residues from whole protein 
so I have used 
make_ndx -f protein.gro -n r_20-50.ndx
 selected  1 & r 20-50 means in whole protein select from res 20-50 
7.g_rms -f 9ns_prot.xtc -n r_20-50.ndx -pbc -s min_wat.gro -o rms_9ns.xvg
  Here I have selected "protein&r_20-50" for group least square fit and
       then selected " group 3(c-alpha)" for RMSD calculation
 
In above mentioned steps did I do any where wrong
I am pasting my md.mdp file
title               =  dpt_prod
constraints         =  hbonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  500000   ; total 250 ps.
nstcomm             =  1
nstxout             =  100
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  1.4
pbc                 =  xyz
comm_grps           =  Protein
; Berendsen temperature coupling is on in two groups
Tcoupl              =  Berendsen
tc-grps             =  Protein   SoL_CL-
tau_t               =  0.1       0.1
ref_t               =  300       300
; isotropic pressure coupling is off
Pcoupl              =  no
pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Energy monitoring
energygrps          =  Protein  SOL_CL-
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300
gen_seed            =  173529
~                          

Waiting for invaluable suggestion
Thanks in advance 
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