Dear All,
I am trying to run a simulation for an ethane molecule in gas phase.
I created this ethane molecule in xleap, and it is for ethane ->
methane perturbation. The input file I have is as follows:
--------------
200 ps simulation with lambda = 1
&cntrl
imin=0,
ntx=1,irest=0,
ntpr=250,ntwr=1000,ntwx=250,
ntc=1,ntf=1,ntb=0,cut=10,
igb=0,
ntr=0,
nstlim=200000,dt=0.001,nscm=1000,nrespa=1,
ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=233,
ntp=0,taup=1,pres0=1,
icfe=1,clambda=1,klambda=6
/
--------------------
Before running this job, I minimised this structure. In any case, when the
above job is run, I am getting an error at 152.750 ps. Here is the error:
--------------------
NSTEP = 152750 TIME(PS) = 152.750 TEMP(K) = 316.18 PRESS =
0.0
Etot = 10.3009 EKtot = 5.6547 EPtot =
4.6462
BOND = 3.4010 ANGLE = 1.1054 DIHED =
0.1398
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
Frac coord min, max: -4.942607998894864E-004 0.500000000000000
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
------------------------------------
As far as I understand, the above error is saying that the molecule is out
of the virtual box sander has created. Does that mean that it is not
important? I dont use any boundary. This is just for testing on something.
I will appreciate if someone can give me more info about this error.
Best,
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Tue Mar 29 2005 - 23:53:01 PST
