rama david wrote:
Dear Gromacs Specialists,
I am very novice to Molecular Simulation study.
I am using GROMACS 4.5.4 version .
I completed some GROMACS tutorials , I not found any
tutorial on Simulated Annealing..
If Any one know the link please give me it..
I make my protocol to work on simulated annealing as follow ...
(I am not writing in detail sorry for that )
1. pdb2gmx ...
2. editconf
3. Solvent Addition
4. Ion addition
5. Energy minimisation
6. simulated annealing
mdp for simulated annealing is as follow...
; 7.3.3 Run Control
title = simulated run
integrator = md ; md integrator
tinit = 0 ; [ps] starting time for run
dt = 0.002 ; [ps] time step
for integration
nsteps = 5000000 ; maximum number of
steps to integrate, 0.002 * 5000000 10 ns
comm_mode = Linear ; remove center of mass translation
comm_grps = Protein Non-Protein ; group(s) for center of
mass motion removal
; 7.3.8 Output Control
nstxout = 100 ; [steps] freq to write
coordinates to trajectory
nstvout = 100 ; [steps] freq to write velocities
to trajectory
nstfout = 100 ; [steps] freq to write forces to trajectory
nstlog = 100 ; [steps] freq to write
energies to log file
nstenergy = 100 ; [steps] freq to write
energies to energy file
nstxtcout = 500 ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision = 500 ; [real] precision to write xtc
trajectory
xtc_grps = System ; group(s) to write to xtc trajectory
energygrps = System ; group(s) to write to energy file
; 7.3.9 Neighbor Searching
nstlist = 5 ; [steps] freq to update neighbor list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions
in all directions
rlist = 1.0 ; [nm] cut-off distance for
the short-range neighbor list
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald electrostatics
rcoulomb = 1.0 ; [nm] distance for Coulomb cut-off
; 7.3.11 VdW
vdwtype = cut-off ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw = 1.4 ; [nm] distance for LJ cut-off
DispCorr = EnerPres ; apply long range dispersion
corrections for energy
; 7.3.13 Ewald
fourierspacing = 0.16 ; [nm] grid spacing for FFT
grid when using PME
pme_order = 4 ; interpolation order for PME, 4 = cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
; 7.3.14 Temperature Coupling
tcoupl = berendson ; temperature
coupling with Nose-Hoover ensemble
tc_grps = Protein Non-Protein ; groups to
couple seperately to temperature bath
tau_t = 0.1 0.1 ; [ps] time
constant for coupling
ref_t = 5 5 ; [K] reference
temperature for coupling
annealing = single single
annealing_npoint = 2 2
annealing_time = 0 20 0 20
annealing_temp = 5 333 5 333
; 7.3.15 Pressure Coupling
pcoupl = parrinello-Rahman ; pressure coupling
where box vectors are variable
pcoupltype = isotropic ; pressure coupling in
x-y-z directions
tau_p = 2.0 ; [ps] time constant
for coupling
compressibility = 4.5e-5 ; [bar^-1] compressibility
ref_p = 1.0 ; [bar] reference
pressure for coupling
; 7.3.17 Velocity Generation
gen_vel = yes ; velocity generation turned off
gen_temp = 5
; 7.3.18 Bonds
constraints = all-bonds ; convert all bonds to constraints
constraint_algorithm = LINCS ; LINear Constraint Solver
continuation = yes ; apply constraints to the
start configuration
lincs_order = 4 ; highest order in the
expansion of the contraint coupling matrix
lincs_iter = 1 ; number of iterations
to correct for rotational lengthening
lincs_warnangle = 30 ; [degrees] maximum angle that
a bond can rotate before LINCS will complain
My Queries
1. Is My mdp file ok ???..please give me a nice protocol..
It is a bad idea to generate velocities and use P-R pressure coupling at the
same time. Such an approach is extremely fragile and your simulation is likely
to crash.
I assume that since you have specified heating over 20 ps of the 10 ns
trajectory that you wish to have the temperature maintained from then on. I
believe Gromacs will handle this elegantly. Pay attention to everything grompp
tells you, in any case.
2.. Should I have to do position restrained MD before SA(simulated annealing)
(If yes then what the temp. should I have to used for NVT and NPT
(as in mdp file has lower 5 K and high 300 k ) )
The answer to this question depends on what you're trying to accomplish with SA.
Position restraints are used to disfavor major structural changes in the
solute as the solvent is equilibrated around it. If SA is your initial step in
equilibration, I would think position restraints can't hurt.
My general protocol is NVT at the initial temperature, SA to heat to the desired
temperature, NPT at the final conditions, and then data collection. You should
base your decision upon what you are wishing to observe and by interpreting how
others have done similar things.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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