rigidTolerance question

From: snoze pa (snoze.pa_at_gmail.com)
Date: Sun Nov 29 2009 - 19:06:15 CST

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,
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

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