I am running v3.3.2. I am running an RNA strand with a homemade potential. When I run a single molecule in a periodic box, the system is fine until one nucleic acid crosses the boundary. THen the entire nucleic acid gets moved to the opposite side of the box. Since there are bonds this results in an exploding system. I am running on 4 processors and am using the following mdp file. Any ideas what is going on? The system runs normally for over 200000 time steps. It runs fine until the boundary issue occurs.
title = Paul Template ;Preprocessor cpp = cpp ;Run control: A leap-frog algorithm for integrating Newton's equations. integrator = sd :time step in femtoseconds dt = 0.0005 ;number of stepsi nsteps = 10000000 ;frequency to write coordinates to output trajectory file nstxout = 0 ;frequency to write velocities to output trajectory file nstvout = 0 ;frequency to write energies to log file nstlog = 1000 ;frequency to write energies to energy file nstenergy = 1000 ;frequency to write coordinates to xtc trajectory nstxtcout = 1000 ;group(s) to write to xtc trajectory xtc_grps = system ;group(s) to write to energy file energygrps = system ;Frequency to update the neighbor list (and the long-range forces, ;when using twin-range cut-off's). nstlist = 50 coulombtype = Cut-off ;Make a grid in the box and only check atoms in neighboring grid cells ;when constructing a new neighbor list every nstlist steps. ns_type = grid ;cut-off distance for the short-range neighbor list rlist = 2.5 ;treatment of electrostatic interactions table_extension = 150.0 rcoulomb = 2.5 epsilon_r = 0 ;treatment of van der waals interactions rvdw = 2.5 ; Periodic boudary conditions in all the directions pbc = full ;Temperature coupling tc-grps = system tau_t = 10.0 ref_t = 100 ;Pressure coupling Pcoupl = no ;Velocity generation gen_vel = yes gen_temp = 100 gen_seed = 12345 ;Constrain all bonds constraints = none ;constraint_algorithm = lincs ;lincs_iter=8 comm_mode = angular thanks -Paul
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