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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