[gmx-users] PR

[pawan raghav]

Thank mark for comments, but I have check the structure after energy
minimization through ramachandran plot and found 82% residues were lies in
core region. After performed position restrained dynamics it reduced to 52%
in core region also 1 bad contact was found. I have taken SPC water model
then add 2 NA+ ions in the solvent, done energy minimization at emtol value
of 2000 kJ/mol and steps for 250. Below is the pr.mdp file for position
restraiuned dynamics, please let me know if any serious flaws. So help me by
giving me the reference.

title = Position restrained of Bcl-2.

integrator = md

define = -DPOSRES

dt = 0.002

nsteps = 100000

nstcomm = 1

nstxout = 250

nstvout = 1000

nstfout = 0

nstlog = 10

nstenergy = 10

nstlist = 5

xtc_grps = protein sol

energygrps = protein sol

ns_type = grid

rlist = 1.0

coulombtype = PME

rcoulomb = 1.0

vdwtype = cut-off

rvdw = 1.4

fourierspacing = 0.135

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

Dispcorr = no

Tcoupl = v-rescale

tc-grps = protein sol NA+

tau_t = 0.1 0.1 0.1

ref_t = 300 300 300

Pcoupl = parrinello-rahman

Pcoupltype = isotropic

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

gen_vel = yes

gen_temp = 300.0

gen_seed = 173529

constraints = all-bonds


-- 
Pawan
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