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..
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 ) )
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
