Hi
We have a problem of equilibrate the system with a protein within DPPC.
We have used dppc128.pdb from Dr. Tielemans website. We have been using
their perl script inflategro.pl to insert our protein. We used position
restraints for the protein as mentioned in Methods 41 (2007) 475-488.
We have tried with a scaling factor of 0,95 and 0,97, and a cut-off
value of 14 to expand the box and 0 to reduce the box (is that ok???).
perl inflategro.pl em1/confout.gro 0.97 DPPC 0 em2/input.gro 5 em2/area.dat
with scaling factor 0.95 23 steps were needed, and with 0,97 39 steps
were followed.
When we have not used position restraints for the protein, and used a
cutoff value of 4 Å, the simulation were performed well even without
annealing.
We have tried to energy minimize the system with steepest descent
method in each step of decreasing the box.
After water soaking, we have tried with both cg and steep energy
minimizations.
The problems we are facing:
- All the energy minimizations are not reaching Fmax < 1000
- When running md, the system explodes, like this:
relative constraint deviation after LINCS:
rms 0.024475, max 1.283027 (between atoms 2654 and 2656)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4615 4616 57.9 0.0896 0.1057 0.1080
...
These are our inputs:
em.mdp for the decrease-box-steps and after water soak:
----------------
cpp = /lib/cpp
define = -DPOSRES
constraints = none
integrator = steep
nsteps = 800
;
; Energy minimizing stuff
;
emtol = 1000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
----------------------
grompp.mdp for md simlulations:
cpp = /lib/cpp
include =
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 3000000 ;6000 ps
nstlog = 5000
nstenergy = 100
nstxout = 50000
nstxtcout = 250
nstvout = 50000
nstfout = 0
xtc_grps = DPPC Cl SOL Protein
energygrps = DPPC Cl SOL Protein
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
tcoupl = Nose-hoover
tc-grps = DPPC Cl SOL Protein
tau_t = 0.1 0.1 0.1 0.1
ref_t = 100 100 100 100
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
gen_vel = yes
gen_temp = 100
gen_seed = 173529
constraints = all-bonds
annealing = single single single single
annealing_npoints = 2 2 2 2
annealing_time = 0 500 0 500 0 500 0 500
annealing_temp = 100 323 100 323 100 323 100 323
pbc = xyz
optimize_fft = yes
unconstrained_start = no
-------------------------
Thankful for all help we can get!
/Edvin and Sujith
--
Fil. Lic. Edvin Erdtman,
PhD. student in Biophysical Chemistry
School of Science and Technology
Modeling and Simulation Center and
Örebro Life Science Center
Örebro University
701 82 Örebro, Sweden
E-mail: [email protected]
Phone: +46 (0)19 30 13 81
Fax: +46 (0)19 30 35 66
Personal web: http://www.oru.se/nt/Edvin_Erdtman
Office: B2313
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