Re: change in box geometry for simulation of pure water

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Thu Aug 28 2008 - 02:11:31 CDT

Hello, thanks for the questions and answers. Here are the answers to the
questions above:

The error was indeed "periodic dimensions have become too small for patch
grid". Restarting is an option, but I do not want the box to become thin in
one direction. Why should that happen? Fluctuations would be fine, but this
is systematic drift in box geometry.

Yes, the box becomes thinner in the z direction, but the box WAS NOT
minimized and pre-equilibrated prior to turning-on usecontantratio and
useflexbilecell

Yes, the dimensions of your boundary conditions are the same as those of
waterbox in initial PDB file.

Thank you for the inputs,

Maria

On Thu, Aug 28, 2008 at 5:58 AM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:

> What, exactly, is the error you get when it crashes? If it's just a
> "periodic dimensions have become too small for patch grid" error, you can
> just restart and be fine. Depending on what kind of system you're trying to
> model you might now want to bother with having useflexiblecell on.
> Peter
>
>
> maria goranovic wrote:
>
>> Hello,
>>
>> I ran a simulation of a box of water with a standard config file using
>> useconstantratio and useflexiblecell. However, the simulation box becomes
>> thinner in one dimension, until the simulation crashes. Why does this
>> happen?
>>
>> Thanks for the suggestions, config file below:
>>
>> !!!!!!!!!!!!!!!!!!!!!!!!!
>> set MOL wat2
>>
>> set temp 310
>>
>> set xbox 39.97
>> set ybox 39.94
>> set zbox 39.94
>>
>> structure ${MOL}.psf
>> coordinates ${MOL}.pdb
>> temperature 0
>> parameters par-combined.prm
>> paraTypeCharmm on
>>
>> outputEnergies 5000
>> outputTiming 5000
>> xstFreq 5000
>> dcdFreq 5000
>> wrapAll on
>> margin 5
>>
>> rigidbonds on
>> timestep 2
>> nonBondedFreq 1
>> fullElectFrequency 1
>> stepsPerCycle 20
>>
>> exclude scaled1-4
>> 1-4scaling 1.0
>> switching on
>> switchDist 10
>> cutoff 12
>> pairlistdist 14
>>
>> cellBasisVector1 $xbox 00.00 00.00
>> cellBasisVector2 00.00 $ybox 00.00
>> cellBasisVector3 00.00 00.00 $zbox
>>
>> #########################################
>> cellOrigin 0.05952 0.09806 -0.1598
>>
>> Pme on
>> PmeGridsizeX 40
>> PmeGridsizeY 40
>> PmeGridsizeZ 40
>>
>> #########################################
>> # PRESSURE AND TEMPERATURE CONTRON
>> #########################################
>>
>> # temperature
>> langevin on
>> langevinDamping 5
>> langevinTemp $temp
>> langevinHydrogen no
>>
>> useflexiblecell yes
>> useconstantratio yes
>> langevinPiston on
>> langevinPistonTarget 1.01325
>> langevinPistonPeriod 100
>> langevinPistonDecay 50
>> langevinPistonTemp $temp
>>
>> binaryoutput on
>> outputname ${MOL}-equil
>>
>> # INITIAL ENERGY
>> minimize 0
>> minimize 5000
>> output ${MOL}-min1
>>
>> #########################################
>> # HEAT
>> #########################################
>>
>> set tem 310
>> langevinTemp $tem
>>
>> for {set p 1 } { $p < 11 } { incr p } {
>> run 1000000
>> output ${MOL}-$p
>> }
>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>

-- 
Maria G.
Technical University of Denmark
Copenhagen

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