Re:

From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Apr 25 2013 - 09:34:41 CDT

the sphere part sounds like a visualization problem, search the list
concerning wrapping. The second part sounds odd, but see what the wrapping
does

On Thu, Apr 25, 2013 at 9:51 AM, Ganesh Shahane <ganesh7shahane_at_gmail.com>wrote:

> Dear all,
> My water box is getting deformed during the equilibration run. It turns
> into a sphere in the first half and then into a rectangular slab-like
> shaped box in the second half of equilibration. Anyone knows whats wrong?
> Initially, the waterbox was created with a minimal distance of 15 angstrom
> between any protein atom and the boundary of the box . Then stepwise
> minimization was performed using CHARMM 36 programme. Then it was minimized
> with 1000 steps of CG as implemented in NAMD and heated from 0 to 300 K.
> Following are my equilibration parameters:-
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 # 2fs/step
> rigidBonds all # needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
> #Velocity reassginment
> rescaleFreq 500
> rescaleTemp 300
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 115.82 0. 0.
> cellBasisVector2 0. 115.46 0.
> cellBasisVector3 0. 0. 77.98
> cellOrigin 0 0 0
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 120
> PMEGridSizeY 120
> PMEGridSizeZ 90
>
>
> #Constant pressure control
> useGroupPressure yes
> useFlexibleCell no
> BerendsenPressure on
> BerendsenPressureTarget 1
> BerendsenPressureCompressibility 0.000049
> BerendsenPressureRelaxationTime 500
> BerendsenPressureFreq 20
>
>
> # Output
> binaryoutput yes
> outputName $outputname
>
> restartfreq 1000
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 1000
> outputPressure 1000
>
> --
> Ganesh
> MSc Bioinformatics
> University of Pune.
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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