[gmx-users] Periodic Boundary conditions

Paul Whitford pwhitfor at ctbp.ucsd.edu
Thu Nov 8 01:41:48 CET 2007

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
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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