AMBER Archive (2005)

Subject: RE: AMBER: vlimit

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Feb 14 2005 - 11:14:56 CST

Dear Gustavo,
 
This is a typical "blowup" situation. There is most likely something wrong
with your system. The very -ve eelec may be symptomatic of this. Is it a
highly charged system? I suspect that during the heating an equilibration
you had restraints on and then you suddenly took them off for the dynamics?
If not then something is very strange since systems rarely blowup after
running 152ps of simulation.
 
To get an idea of what is going on you can re-run the simulation that blows
up with ntwx=1. This will write to the mdcrd file on every step. You can
then visualise this in something like VMD and you'll be able to see what
happens.
 
All the best
Ross
 

    In performing a molecular dynamic, an error appeared in the production
phase. I had already done the heating and equilibration, and when I started
the dynamics, the following message appeared:
 
NSTEP = 42000 TIME(PS) = 152.000 TEMP(K) = 298.55 PRESS = 0.0
 Etot = -85755.4198 EKtot = 24869.6218 EPtot = -110625.0416
 BOND = 29079.6707 ANGLE = 3824.3590 DIHED = 3089.8948
 1-4 NB = 1582.6777 1-4 EEL = 5825.1186 VDWAALS = 59165.1805
 EELEC = -213191.9429 EHBOND = 0.0000 RESTRAINT = 0.0000
 
---------------------------------------------------------------------------- 

--
 vlimit exceeded for step  42931; vmax =   37.657011
 vlimit exceeded for step  42932; vmax =   57.1317451
 vlimit exceeded for step  42933; vmax =   21.2684893
 vlimit exceeded for step  42934; vmax =   144.750365
 vlimit exceeded for step  42935; vmax =   22.9808825
 vlimit exceeded for step  42936; vmax =   26.6725465
 vlimit exceeded for step  42955; vmax =   22.2635511
 vlimit exceeded for step  42967; vmax =   20.5759413
 vlimit exceeded for step  42977; vmax =   20.5195492
 vlimit exceeded for step  42988; vmax =   21.3032238
   KE Trans =     0.1209   KE Rot =     0.0082   C.O.M. Vel =    0.001169
   Translational and rotational motion removed
   KE Trans =     0.0000   KE Rot =     0.0000   C.O.M. Vel =    0.000000
 vlimit exceeded for step  43006; vmax =   20.4031066
 vlimit exceeded for step  43007; vmax =   20.4345712
 vlimit exceeded for step  43008; vmax =   2024.19554
 vlimit exceeded for step  43009; vmax =   23.2434449
 
The last lines of the output are :
 
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.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error
                                      
If someone knows what is happening, please let me know
Thanks
 
 
 

 

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