Dear AMBER users,
I am trying to calculate the energies of a solvated glucose with TIP5P water in truncated octahedron box. I am doing a one step energy minimization to evaluate the energy of the system in the trajectory. The system has the box dimension of over 60 angstrom. There are no periodic boundaries in either topology and trajectory file. The energy calculation would die even at the first step.
The error is:
minimizing coord set # 1
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
Frac coord min, max: 0.45443913178870859 1.0144599523215547
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
The input file I have is :
Minimization everything
&cntrl
imin=5, dielc=1,ntb=0,
maxcyc=1,
cut=99999,
drms=0.01,
/
END
Can anyone help me?
Thank you very much!
Best regards,
Xiao
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Received on Sun Mar 03 2019 - 01:00:02 PST
