On 24/07/2012 2:37 PM, tarak karmakar wrote:
Dear All,
In a protein simulation I imposed one bond constraint by
incorporating the "[constraints]" block in topology file. On the other
hand in .mdp file I have imposed constraints for the covalent hydrogen
bonds by implementing the LINCS algorithm. After a short equilibration
run I see the bond length is fixed [served my purpose], but then what
algorithm it's making use of to constraint the specified bond ?
You told mdrun to use the LINCS algorithm for constraints. You created
constraints in two different ways. It's all the same from there.
Mark
The .mdp file is given below
Thanks.
......................................................................................................................................................................................
; 7.3.2 Preprocessing
;define = -DPOSRES ; defines to pass to the preprocessor
; 7.3.3 Run Control
integrator = md ; md integrator
tinit = 0 ; [ps] starting time for run
dt = 0.001 ; [ps] time step for integration
nsteps = 50000 ; maximum number of
steps to integrate, 0.001 * 50,000 = 500 ps
comm_mode = Linear ; remove center of
mass translation
nstcomm = 1 ; [steps] frequency of
mass motion removal
comm_grps = Protein Non-Protein ; group(s) for center
of mass motion removal
; 7.3.8 Output Control
nstxout = 1000 ; [steps] freq to write
coordinates to trajectory
nstvout = 1000 ; [steps] freq to write
velocities to trajectory
nstfout = 1000 ; [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 = 100 ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision = 100 ; [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 = 1 ; [steps] freq to update neighbor list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions
in all directions
rlist = 0.8 ; [nm] cut-off distance for
the short-range neighbor list
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald electrostatics
rcoulomb = 0.8 ; [nm] distance for Coulomb cut-off
; 7.3.11 VdW
vdwtype = cut-off ; twin-range cut-off with
rlist where rvdw >= rlist
rvdw = 0.8 ; [nm] distance for LJ cut-off
DispCorr = EnerPres ; apply long range dispersion
corrections
; 7.3.13 Ewald
fourierspacing = 0.12 ; [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 = Berendsen ; temperature coupling
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 = 300 300 ; [K]
reference temperature for coupling
; 7.3.17 Velocity Generation
gen_vel = yes ; generate velocities
according to Maxwell distribution of temperature
gen_temp = 300 ; [K] temperature for Maxwell
distribution
gen_seed = -1 ; [integer] used to initialize
random generator for random velocities
; 7.3.18 Bonds
constraints = h-bonds ; constraining covalent h-bonds
constraint_algorithm = LINCS ; LINear Constraint Solver
continuation = no ; no = 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
--
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