[gmx-users] PBC, lincs and bonds breaking

[David van der Spoel]

Paul Whitford wrote:
> 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. '
try pbc=full

> 
> 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
> 
> -Paul
> 
> MDP
> 
> title                    = Paul Template
> ;Preprocessor
> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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