Re: PME fails no matter what

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Tue Jul 29 2008 - 00:17:41 CDT

serched archive, changed addition to basis vectors to 0.25A -- still,
no solution to the problem. it runs first 500 steps and gives the
error.

disabled line with minimization, then RATTLE complained. this is
getting annoying, nothing in comparison to the ease of the water
sphere simulations.

i have a general question. i am simulating 30 residue peptide and
simulations in water sphere were just perfect for me, but my boss said
that for consistency i need to run PBC of peptide in water box.

can PBC really so greatly affect simulations? what are the cases when
PBC important? we are interested in just folding the peptide.

On Tue, Jul 29, 2008 at 12:50 AM, Joshua Adelman <jadelman_at_berkeley.edu> wrote:
> 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
> ------------------------------------------------------------------------------------------------------
>
>
>
>

-- 
Roman Petrenko.
Physics Department
University of Cincinnati

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