Dear Amber users,
I am facing this error in my system during minimisation which is made
by joining the residues.1-4 EEL is very high. how I can change virtual
box size. My system is not breaking in constituent residues. Is this
due to the reason my residues charge derivation is not correct? Net
charge of the system being 0.0010018. My residues are having charge of
0.000002, but large number of residues when joined together generate
the charge of 0.001. Is the large 1-4eel value, due to net charge not
being close to zero (0.00006)?
NSTEP
ENERGY
RMS
GMAX
NAME NUMBER
150
-4.4854E+07 3.5453E+11
2.9984E+13
O1 7650
BOND = 14042.8945
ANGLE = 19616.0792
DIHED = 7618.1747
VDWAALS = 12679.3423
EEL = 19162.7085
HBOND
= 0.0000
1-4 VDW = 5502.1137 1-4 EEL =
************* RESTRAINT
= 0.0000
Frac coord min, max:
-74352.1646571339
1254553.54504669
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
please suggest
regards,
JIomm
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Received on Wed Apr 14 2010 - 05:00:03 PDT
