Re: PME fails no matter what

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jul 29 2008 - 11:38:20 CDT

Hi Roman,
please note, since it's important to understand what the actual problem
here is, that this is not a problem with PME but rather one with your
periodic cell (and, most notably, the fact that it is shrinking
significantly early on in the simulation). You may want to run writing
an xst file every timestep and then check whether your cell shrinks
rapidly after minimization -- it probably does. If this is the case, you
will need to either follow the advice of restarting from a recent
checkpoint, or reduce your initial periodic cell size to be closer to
what the actual, equlibrated cell size will be. How did you solvate your
input system?
Best,
Peter

Roman Petrenko wrote:
> Dear all,
> my system size is (min and max)
> {-16.3659992218 -18.3840007782 -13.1579999924} {17.0270004272
> 17.5310001373 7.91699981689}
>
> the center is
> 0.253832936287 -0.271096855402 -2.62966871262
>
> additionally i add 2.5A in each direction for the basis vectors
> TO_NAMD:cellBasisVector1 35.892999649 0. 0.
> TO_NAMD:cellBasisVector2 0. 38.4150009155 0.
> TO_NAMD:cellBasisVector3 0. 0 23.5749998093
> TO_NAMD:cellOrigin 0.253832936287 -0.271096855402 -2.62966871262
> TO_NAMD:wrapAll on
>
> now minimization is ok for 100 steps, but the main run (it is NPT
> simulation) fails no matter what parameter i put for PMEGridSize. i've
> tried starting from 32 to 90.
>
> TO_NAMD:PME yes
> TO_NAMD:PMEGridSizeX 32
> TO_NAMD:PMEGridSizeY 32
> TO_NAMD:PMEGridSizeZ 32
>
>
> every time i get this error:
> ------------- 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.
> ------------------------------------------------------------------------
>
> I can't follow these instructions, because my useFlexibleCell is aready off
>
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> Please, help.
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:06 CST