[gmx-users] PBC, lincs and bonds breaking

Paul Whitford pwhitfor at ctbp.ucsd.edu
Sat Oct 27 00:46:55 CEST 2007

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.

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



title                    = Paul Template
cpp                      = /lib/cpp
;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator               = sd
:time step in femtoseconds
dt                       = 0.0005
;number of steps
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          = 15.0
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
tcoupl                   = berendsen
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             = all-bonds
constraint_algorithm    = lincs
comm_mode = linear
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