Re: PME fails no matter what

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Tue Jul 29 2008 - 12:00:11 CDT

To follow up on this, Peter helped me with a similar problem a number
of months ago. The complete thread is found here:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7256.html

Basically the solution was check the xst file and then take steps to
make sure there wasn't a large change in the cell size. Some things
you might want to try:
- Slowly heating the system during equilibration
- Equilibrating the solvent while restraining the protein
- Start with no rigid bonds and a small time step (for a particularly
nasty system I started with 0.5fs, brought it to 1 fs and then once I
was confident that things were ok, then turned rigidBonds on and used
2.0 fs)

Hope that helps.

Josh

On Jul 29, 2008, at 9:38 AM, Peter Freddolino wrote:

> 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.
>>
>>
>>
>>
>

------------------------------------------------------------------------------------------------------
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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