On 1/1/13 10:53 AM, Shima Arasteh wrote:
If I tell you that I changed the constraints and now the NVT is running,
would that be ok? However I don't know the scientific reason of this incident!
But I bring you the EM.mdp as follow:
define = -DSTRONG_POSRES
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 100.0 ; Stop minimization when the maximum force < 100.0
kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long
range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range
forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
And the NVT.mdp as follow (after change of all-bond constraint to h-bond):
title = NVT equilibration for dimer-POPC - CHARMM36
define = -DPOSRES ; Protein is position restrained (uses the
posres.itp file information)
; Parameters describing the details of the NVT simulation protocol
integrator = md ; Algorithm ("md" = molecular dynamics [leap-frog integrator];
"md-vv" = md using velocity verlet; sd = stochastic dynamics)
dt = 0.002 ; Time-step (ps)
nsteps = 50000 ; Number of steps to run (0.002 * 50000 = 100 ps)
; Parameters controlling output writing
nstxout = 1 ; Write coordinates to output .trr file every 2 ps
nstvout = 1000 ; Write velocities to output .trr file every 2 ps
nstenergy = 1000 ; Write energies to output .edr file every 2 ps
nstlog = 1000 ; Write output to .log file every 2 ps
; Parameters describing neighbors searching and details about interaction
calculations
ns_type = grid ; Neighbor list search method (simple, grid)
nstlist = 5 ; Neighbor list update frequency (after every given
number of steps)
rlist = 1.2 ; Neighbor list search cut-off distance (nm)
rlistlong = 1.4
rcoulomb = 1.2 ; Short-range Coulombic interactions cut-off distance
(nm)
rvdw = 1.2 ; Short-range van der Waals cutoff distance (nm)
pbc = xyz ; Direction in which to use Perodic Boundary Conditions
(xyz, xy, no)
vdwtype = switch
rvdw_switch = 0.8
; Parameters for treating bonded interactions
continuation = no ; Whether a fresh start or a continuation from a
previous run (yes/no)
constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE)
constraints = h-bonds ; Which bonds/angles to constrain (all-bonds /
hbonds / none / all-angles / h-angles)
lincs_iter = 1 ; Number of iterations to correct for rotational
lengthening in LINCS (related to accuracy)
lincs_order = 4 ; Highest order in the expansion of the constraint
coupling matrix (related to accuracy)
; Parameters for treating electrostatic interactions
coulombtype = PME ; Long range electrostatic interactions treatment
(cut-off, Ewald, PME)
pme_order = 4 ; Interpolation order for PME (cubic interpolation is
represented by 4)
fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME
(nm)
; Temperature coupling parameters
tcoupl = v-rescale ; Modified Berendsen thermostat using
velocity rescaling
tc-grps = Protein POPC SOL_CL ; Define groups to be coupled
separately to temperature bath
tau_t = 0.1 0.1 0.1 ; Group-wise coupling time constant (ps)
ref_t = 310 310 310 ; Group-wise reference temperature (K)
; Pressure coupling parameters
pcoupl = no ; Under NVT conditions pressure coupling is not done
; Miscellaneous control parameters
; Dispersion correction
DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for
vdW cut-off
; Initial Velocity Generation
gen_vel = yes ; Generate velocities from Maxwell distribution at
given temperature
gen_temp = 310 ; Specific temperature for Maxwell distribution (K)
gen_seed = -1 ; Use random seed for velocity generation (integer; -1
means seed is calculated from the process ID number)
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm = 1 ; COM removal frequency (steps)
comm_mode = Linear ; Remove COM translation (linear / angular / no)
comm_grps = Protein_POPC SOL_CL ; COM removal relative to the specified
groups
Any suggestions please?
Yes, the problem is the constraints. You minimized without any, and then
constrained all bonds during NVT. During EM, you can get bad geometry sometimes
when atomic clashes force atoms to move in bad ways. Without constraints, mdrun
doesn't object to these deformations. Then, as you see from step zero of the
NVT, trying to apply constraints to these bad areas immediately fails.
-Justin
--
========================================
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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