Re: Problems restarting an amber simulation

From: Guanglei Cui (amber.mail.archive_at_gmail.com)
Date: Wed Jan 16 2008 - 14:35:30 CST

I found it confusing that you tried to switch to NAMD from AMBER but
consulted Gromacs manual. Plus, if you don't make a velocity file out
of AMBER restart and include that in your NAMD input, you're not
really restarting the previous run. Anyway, if your box is
orthorhombic, you only specify the length in each dimension as
cellBasisVector, for example, 68.119 0 0. You can find box information
from the end of your AMBER restart. I hope this helps.

On Jan 16, 2008 12:04 PM, Seth Lilavivat <sethl_at_gatech.edu> wrote:
> 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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