Re: rigidTolerance question

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Nov 29 2009 - 19:51:28 CST

On Sun, 2009-11-29 at 19:06 -0600, snoze pa wrote:
> Dear NAMD users,
>
> I have a question abot the value of rigidTolerance. When I am using a
> value equal to 0.00000001 then my simulation crashed after 100000
> step. A close analysis shows that the water is pushed wiped out from
> one side by 2A at least during equilibration. And the message it print
> is
>
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,

i think those two things are mostly unrelated. your system seems to
be shrinking a lot and a restart after every few ten thousand steps is
recommended anyways until the system doesn't shrink much anymore.

axel.

> increase margin, or disable useFlexibleCell for liquid simulation.
> 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.
> [2] Stack Traceback:
> [0] CmiAbort+0x7f [0xa6efe5]
> [1] _Z8NAMD_diePKc+0x62 [0x508252]
> [2] _ZN9HomePatch13doMarginCheckEv+0x235 [0x885455]
> [3] _ZN9HomePatch14positionsReadyEi+0x63 [0x8841dd]
> [4] _ZN9Sequencer17runComputeObjectsEii+0xad [0x935e03]
> [5] _ZN9Sequencer9integrateEv+0x1186 [0x932962]
> [6] _ZN9Sequencer9algorithmEv+0x32e [0x92f46e]
> [7] _ZN9Sequencer9threadRunEPS_+0xe [0x93c832]
> [8] CthStartThread+0x20 [0x9e0d6a]
>
> However, when I do the simulation with rigidTolerance = 0.000001 then
> there is no problem in equilibration.
>
> Any Idea why my simulation crashed in first case and run in second
> case. What is the right value for rigidTolerance?.
>
> Thank you,
>
> S
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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