I am trying to simulate my own structure based simulation using 3.3.2.
I have developed the forcefield and it works fine without periodic
boundary conditions. When I use pbc=xyz atoms that are connected in
the [bonds] section of the topology get broken. What happens is 1 of
the two atoms will cross the boundary and that single atom will get
placed on the opposite side of the box. In the next step, the system
will explode. If I use lincs, I get error messages about angles
getting changed and that lincs can not satisfy the constraint. I get
the same issue with shake. when i run lincs, the structure is output
before the errors and after, so I can see that 1 atom is placed on the
opposite side of the box and that is the same atom that I get lincs
errors about. Below is my .mdp file. <br><br>I saw the same errors have been posted when people try to run
infinite polymers, but I didn't see any resolution to this. Any help
would be appreciated. thanks<br><br>-Paul<br><br>MDP<br><br>title = Paul Template
<br>;Preprocessor<br>cpp = /lib/cpp<br>;Run control: A leap-frog algorithm for integrating Newton's equations.<br>integrator = sd<br>:time step in femtoseconds<br>dt =
0.0005<br>;number of steps<br>nsteps = 10000000<br>;frequency to write coordinates to output trajectory file<br>nstxout = 0<br>;frequency to write velocities to output trajectory file<br>
nstvout = 0<br>;frequency to write energies to log file<br>nstlog = 1000<br>;frequency to write energies to energy file<br>nstenergy = 1000<br>;frequency to write coordinates to xtc trajectory
<br>nstxtcout = 1000<br>;group(s) to write to xtc trajectory<br>xtc_grps = system<br>;group(s) to write to energy file<br>energygrps = system<br>;Frequency to update the neighbor list (and the long-range forces,
<br>;when using twin-range cut-off's).<br>nstlist = 50<br>coulombtype = Cut-off<br>;Make a grid in the box and only check atoms in neighboring grid cells<br>;when constructing a new neighbor list every nstlist steps.
<br>ns_type = grid<br>;cut-off distance for the short-range neighbor list<br>rlist = 2.5<br>;treatment of electrostatic interactions<br>table_extension = 15.0<br>rcoulomb =
2.5<br>epsilon_r = 0<br>;treatment of van der waals interactions<br>rvdw = 2.5<br>; Periodic boudary conditions in all the directions<br>pbc = full<br>;Temperature coupling
<br>tcoupl = berendsen<br>tc-grps = system<br>tau_t = 10.0<br>ref_t = 100<br>;Pressure coupling<br>Pcoupl = no<br>;Velocity generation
<br>gen_vel = yes<br>gen_temp = 100<br>gen_seed = 12345<br>;Constrain all bonds<br>constraints = all-bonds<br>constraint_algorithm = lincs<br>comm_mode = linear
<br>