Re: PME fails no matter what

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Jul 29 2008 - 14:41:50 CDT

I'm adding my 2 cents here. I have had this problem in the past when I
specified the cell dimensions to be bigger than what the water box is in
reality. In your configuration I see that the specified cellBasisVectors
are larger than the result of minmax. Thus I would try reducing them to:

TO_NAMD:cellBasisVector1 34.0 0. 0.
TO_NAMD:cellBasisVector2 0. 36.0 0.
TO_NAMD:cellBasisVector3 0. 0 25.0

If that doesn't work try reducing one or all of them of 1 A. During
minimization water molecules which are outside the specified box will be
adjusted.

Also, I like having the center of the box at the origin of the system. It
probably doesn't matter but it might give more clarity. To do that use
VMD:

# Center the solvated system (the following two lines are a single line)
[atomselect top "all"] moveby [vecscale -1 [measure center [atomselect top
"all"]]]

Remember to get rid of:

TO_NAMD:cellOrigin 0.253832936287 -0.271096855402 -2.62966871262

Good luck,

         Gianluca

> 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.
>>
>>
>>
>>
>
>
>

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