[gmx-users] Periodic Boundary conditions

Berk Hess gmx3 at hotmail.com
Thu Nov 8 13:49:04 CET 2007

The problem is the combination of pbc=full and comm_mode = angular.
With pbc=xyz it will work.

We will add a check for this.

Anyhow, pbc=full is only useful when you have periodic molecules.


>From: "Paul Whitford" <pwhitfor at ctbp.ucsd.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>Subject: [gmx-users] Periodic Boundary conditions
>Date: Wed, 7 Nov 2007 16:41:48 -0800
>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 
>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
>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
>comm_mode = angular

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