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