On 21/11/2010 9:09 PM, pawan raghav wrote:
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
A smaller timestep during equilibration will better help the integration
cope with anything that is not very happy.
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+
Those groups are bad. See
http://www.gromacs.org/Documentation/Terminology/Thermostats
Mark
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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