Re: PME fails no matter what

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Fri Aug 01 2008 - 18:02:03 CDT

Thank you guys for your explanations of the problem.
As was suggested I slowly equilibrated the system while heating it to
the needed temperature.
And that solved the problem.

Here is my execution script from namd.conf file
----------------------------------------------------
# Minimization
minimize $minimize_steps
reinitvels $temperature

# Slowly heat the system
for {set i 15} {$i < $temperature} {incr i 15} {
set tempr $i
langevinTemp $tempr
run 100
}

# Run at needed temperature
langevinTemp $temperature
run $run_steps ;# 3ns
----------------------------------------------------

On Tue, Jul 29, 2008 at 1:00 PM, Joshua Adelman <jadelman_at_berkeley.edu> wrote:
> 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
> ------------------------------------------------------------------------------------------------------
>
>
>
>

-- 
Roman Petrenko.
Physics Department
University of Cincinnati

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