Problems restarting an amber simulation

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Wed Jan 16 2008 - 11:04:14 CST

Dear NAMD users,

I have a simulation that was stable under AMBER 8 and wanted to restart it
using NAMD. I assigned the Cell Basis Vectors according to page 13 of the
GROMACS 3.3 manual. I am relatively new to NAMD and am not sure why I am
getting the error below. I have also experimented with the margin size and
get the same result.

ERROR: Constraint failure in RATTLE algorithm for atom 246!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 61!
ERROR: Constraint failure; simulation has become unstable.
FATAL ERROR: Periodic cell has become too small for original patch grid!

-------------------------------------------------------------------------------------------------------------------------------------

My config file is as follows:

rigidTolerance 0.0005 # Default is 0.00001
numsteps 5000 # Num of total steps
outputEnergies 50 # Energy output frequency
restartfreq 1000 # Restart file frequency
DCDfreq 100 # Trajectory file frequency
timestep 2 # in unit of fs
temperature 300 # Initial temp for velocity assignment
cutoff 10
switching off # Turn off the switching functions

PME on # Use PME for electrostatic calculation
# Orthogonal periodic box size
cellBasisVector1 66.119 22.040 -22.040
cellBasisVector2 0 7.666 3.833
cellBasisVector3 0 0 6.639
cellOrigin 29.845 29.562 29.864
PMEGridSizeX 70
PMEGridSizeY 70
PMEGridSizeZ 70

amber on # Specify this is AMBER force field
parmfile telomere-aza3-wat.prmtop # Input PARM file
ambercoor md1.rst # Input coordinate file
outputname test-10ps # Prefix of output files
exclude scaled1-4
1-4scaling 0.833333 # =1/1.2, default is 1.0

Thank you for your help,
Seth

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