Re: PME fails no matter what

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Mon Jul 28 2008 - 23:50:19 CDT

I don't think you want to be adding that much 'padding' to the basis
vectors. Generally I add a fraction of an angstrom beyond my system
size. I would try decreasing your cellBasisVector's and give it
another shot.

Also if you search your error on the namd-l archive, there are several
discussions with solutions. I would always advise searching that
resource first since many questions are already answered there.

Josh

On Jul 28, 2008, at 9:29 PM, 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.
>
>
>
> --
> Roman Petrenko.
> Physics Department
> University of Cincinnati
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
------------------------------------------------------------------------------------------------------

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