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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Received on Mon Feb 14 2005 - 17:53:01 PST