AMBER Archive (2007)

Subject: AMBER: Fwd: System extending beyond of (non existent) virtual box

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Sep 08 2007 - 03:33:34 CDT

The day after, empirically following the error message, I have solved the issue
by running minimization for a lesser number of step than to create problems,
then minimization at full extent. Stepwise heating and amd1 md went on
regularly.
francesco pietra

--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Date: Fri, 7 Sep 2007 10:17:36 -0700 (PDT)
> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: System extending beyond of (non existent) virtual box
> To: Amber <amber_at_scripps.edu>
>
> Consultation of the archive notwithstanding I am puzzled by the following
> message at the end of minout:
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3900 4.8716E+01 6.1030E-04 4.2568E-03 C 19
>
> BOND = 0.9194 ANGLE = 3.1885 DIHED = 25.0950
> VDWAALS = -3.3985 EEL = -17.5549 HBOND = 0.0000
> 1-4 VDW = 7.8486 1-4 EEL = 32.6179 RESTRAINT = 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3950 4.8716E+01 2.0648E-04 1.0189E-03 C1 21
>
> BOND = 0.9194 ANGLE = 3.1885 DIHED = 25.0950
> VDWAALS = -3.3985 EEL = -17.5549 HBOND = 0.0000
> 1-4 VDW = 7.8486 1-4 EEL = 32.6179 RESTRAINT = 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4000 4.8716E+01 1.5402E-04 4.4388E-04 H20 37
>
> BOND = 0.9194 ANGLE = 3.1884 DIHED = 25.0951
> VDWAALS = -3.3985 EEL = -17.5548 HBOND = 0.0000
> 1-4 VDW = 7.8486 1-4 EEL = 32.6179 RESTRAINT = 0.0000
> Frac coord min, max: -2.60554141237325 3.54373637786288
> The system has extended beyond
> the extent of the virtual box.
> Restarting sander will recalculate
> a new virtual box with 30 Angstroms
> extra on each side, if there is a
> restart file for this configuration.
> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> Atom out of bounds. If a restart has been written,
> restarting should resolve the error
>
> minin:
>
> Classical minimization in vacuum
> &cntrl
> imin=1, ncyc=4000, maxcyc=10000,
> ntb=0, ntc=1, ntf=1,
> cut=25
> /
>
>
> Identical error message with "cut=999".
>
> The procedure was launched with
>
> mpirun -np 1 $AMBERHOME/exe/sander.MPI, as it deals of a 39-atoms molecule,
> single residue. I used before those inputs with a variety of molecules,
> bigger
> and more complicated than present one. prepin was obtained with antechamber,
> which recognized everything.
>
> The molecule was carefully minimized with MMFF94 before input to antechamber,
> and prmtop inpcrd give the correct structure. I can also add that the input
> pdb
> could be minimized DFT with a number of functionals and basis set with no
> problem.
>
> In neither mpirun was a restart file produced, so that I can't check
> graphically what happened, in particular what has moved apart in the
> molecule.
> Though I feel that it must be a trivial problem, I am unable to come out.
>
> Thanks for help.
>
> francesco pietra
>
>
>
>
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