Hi everyone,
I am running MD simulations using Amber18-Ambertools 19 with CHARMM forcefield. It seems like my protein complex is moving out of PBC box during simulation.
I tried "autoimage" and also "image with center" within the production run script but coming with the following error:
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
Here is a piece of Production run Script:
cd $MYDIR/$SUBDIR1
export CUDA_VISIBLE_DEVICES="0"
cat > image.in <<EOF
parm tem1-mem.parm7
trajin md$x.nc
center :1-264 mass origin
image familiar com :1-264
trajout md$x0.nc
go
EOF
cpptraj < image.in &> image.out
$MYEXE -O -i md10.i -o md$x.log -p tem1-mem.parm7 -c md$x0.rst -x md$x.nc -r md$x.rst &
But when I run image + center separately on a single coordinate file, it run smoothly without error but the complex blink for several frames and then disappears from the visualizer.
Here is the script: parm tem1-mem.parm7
trajin md10.nc
center :1-264 mass origin
image familiar com :1-264
trajout md10.nc
go
Please suggest something about this.Thanks,Hira
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Received on Tue Oct 08 2019 - 04:30:02 PDT
