eRROR OBTAINED DURING NVT: Water molecule starting at atom 673675 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. NVT CONDITIONS WERE :
n for B2AR-POPC system 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 = 250000 ; Number of steps to run (0.002 * 250000 = 500 ps) ; Parameters controlling output writing nstxout = 1000 ; 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) 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) ; 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 = all-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 2 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 8 ; 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 DOPC SOL_NA ; 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 = 300 300 300 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = no ; Under NVT conditions pressure coupling is not done -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics & Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.