Re: Bond energy become Zero!!!

From: Peter Freddolino (beakerbreaker_at_gmail.com)
Date: Thu Jun 05 2008 - 08:25:55 CDT

Hi Ming,
are you using rigidbonds? That's the only reason I can think of that
your bond energy would be zero (since all your bonds involve hydrogens).
If you're using rigidbonds this is not related to the crash you're
seeing. Have you tried restarting the simulation after the crash using
the periodic cell from before the crash, or starting the simulation with
a smaller periodic cell? The usual cause for this error is your system
shrinking significantly under the influence of the barostat during early
stages of the simulation.
Best,
Peter

Ming wrote:
> Dear all,
> I was trying to parameterize a novel ligand and apply it to NAMD. I've done some
> tests and I can get the parameters for CH4 from Gaussian calculation. I use the
> paratool plugin of VMD 1.8.6 to extract force constants and then integrate them
> into a Charmm standard parameter file. After that, I solvated it with a water box
> (18 X 18 X 18) and then minimized the system for 10000 steps with PBC. The
> calculation ran well. However, when I try to MD it, a strange problem emerged: The
> bond energy item equaled ZERO from the very beginning (see below), and the angle
> energy became very small comparing with those in the minimization steps. By the
> way, the bond energy in the minimization step was not zero.
>
>
> ############### In the MIN step ##########################
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC KINETIC
> TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 500 51.7171 37.1374 0.0000 0.0000
> -1800.1506 250.0243 0.0000 0.0000 0.0000
> -1461.2718 0.0000 -1461.2718 -1461.2718 0.0000
> -1585.4762 -1307.9887 8000.0000 -1585.4762 -1307.9887
>
>
> ############# IN the MD step ###########################
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC KINETIC
> TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 3000 0.0000 0.4894 0.0000 0.0000
> -1506.9501 145.7842 0.0000 0.0000 252.1150
> -1108.5616 298.1669 -1108.3788 -1107.1115 308.1840
> -49.1478 -32.1334 4300.4393 -70.3853 -69.2148
>
>
>
> After several steps, the simulation crashed!
> These are the Error message:
>
> #####################################################
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> Charm++ fatal error:
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
>
> Stack Traceback:
> [0] _ZN9HomePatch13doMarginCheckEv+0x1d7 [0x825041f]
> [1] _ZN9HomePatch14positionsReadyEi+0x6e [0x824ec6a]
> [2] _ZN9Sequencer17runComputeObjectsEii+0xcc [0x82bbb8c]
> [3] _ZN9Sequencer9integrateEv+0xb04 [0x82c06c4]
> [4] _ZN9Sequencer9algorithmEv+0x334 [0x82bb490]
> [5] _ZN9Sequencer9threadRunEPS_+0xc [0x82ccb4c]
> [6] namd2 [0x831a849]
> [7] Charm++ Runtime: Converse thread (qt_args+0x72 [0x8394b92])
>
> ############################################################
>
>
> I've tried to increase the PBC and margin, however, these didn't work for me.
> Any suggestions? I thought the problem caused by the Zero bond energy but I am not
> sure...This reallu confused me!! Anyone can save me???? Many thanks!!!!!!
>
> PS: the topology and parameter calculated by mysely for CH4 are attached,the psf
> and pdb I used in the test were also included.
>
>
>
>
>
>
>

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