Hi all,
I am running an LES calculation in a protein with 100 copies of ammonia
molecules inside the protein to find possible tunnels( I am trying to
saturate a tunnel that is quite long). Earlier MD simulations ended up in
some ammonias leaking out of the structure giving me the error
Frac coord min, max: 0.1576021732346622 1.000169854745692
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
Then I put a shell of water molecules using
solvateShell protein 4.0 0.8
which added 699 water molecules around the protein. This was done hoping
that it would stop the leakage of ammonia molecules due to hydrogen bonds.
Now the problem is even without the ammonia molecules flying out of the
structure, the same error is given in a very short period of time (like 2
picoseconds) and the simulation stops. I tried restarting as told in the
error message. Then the system runs for about another 2 picoseconds
(sometimes 1 picosecond) and throws the same error again. There is no
apparent huge change in the structure. This problem has been pestering me
for about a week now. Your advice is highly appreciated.
Thank you
Sajeewa Dewage
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 25 2012 - 10:00:02 PDT
