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 ======================================== -- 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!

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