On 7/28/12 1:49 PM, tarak karmakar wrote:
Dear All ,
I wanted to keep all the molecules other than water fixed [
positiion restraints]. So for that I have performed short NVT
[simulation with DEPOSRE] after minimization, but while seeing the
movie of the trajectory in VMD I see the protein backbone is moving.
So did I miss something prior to the simulation. The nvt.mdp file
is given below
Well -DEPOSRE is going to act differently than -DPOSRES. Check what your
topology expects. For a .top written by pdb2gmx, -DPOSRES is correct based on
the default #include statement. Check carefully for typos or any incorrect
modifications you have made for the topology.
-Justin
; 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 = 0.0005 ; [ps] time step for integration
nsteps = 400000 ; maximum number of
steps to integrate, 0.0005 * 40,000 = 2 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 = 5000 ; [steps] freq to write
coordinates to trajectory
nstvout = 5000 ; [steps] freq to write
velocities to trajectory
nstfout = 5000 ; [steps] freq to write forces
to trajectory
nstlog = 5000 ; [steps] freq to write
energies to log file
nstenergy = 1000 ; [steps] freq to write
energies to energy file
nstxtcout = 1000 ; [steps] freq to write
coordinates to xtc trajectory
xtc_precision = 1000 ; [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 = all-bonds ; constraining all 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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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