From: Rachel Ruskin (rsrusk_at_gmail.com)
Date: Mon Feb 15 2010 - 23:48:00 CST
Never mind; I solved this problem by changing the coordinates of the CellOrigin.
On Mon, Feb 15, 2010 at 5:24 PM, Rachel Ruskin <rsrusk_at_gmail.com> wrote:
> Dear NAMD users,
>
> I am running MD on a protein and membrane system surrounded by a
> waterbox. Before I start minimization, the protein is completely
> surrounded by the waterbox; afterwards, the protein and membrane are
> translated 10 angstroms in the negative z direction, while the
> waterbox remains where it was. The waterbox remains rectangular; there
> is just 10 A of protein sticking out on the negative z side. My
> configuration file follows. Should I attach any other files to make
> this problem easier to diagnose?
> I do not understand why the protein and membrane are translated like
> this instead of remaining inside the waterbox as they should. Does
> this have to do with centering of my periodic cell? Why would that
> differentially affect the protein and water?
>
> Thank you for your time,
>
> Rachel Ruskin
>
>
> # Minimization of 510 Kv Channel in a waterbox
> # with .10 M ions
>
> structure 510_before.psf
> coordinates 510_before.pdb
>
> set temperature 310
> set outputname 510_min1
>
> firsttimestep 0
>
> # Input
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2 ;
> rigidBonds none ;
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
> langevinTemp $temperature
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 162.0 0.0 0.0
> cellBasisVector2 0.0 162.0 0.0
> cellBasisVector3 0.0 0.0 118.0
> cellOrigin 25.7 27.3 16.0
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 180
> PMEGridSizeY 180
> PMEGridSizeZ 120
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.0
> langevinPistonDecay 50.0
> langevinPistonTemp $temperature
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 100
> outputPressure 100
>
> # Temperature reassignment
>
> reassignFreq 1000
> reassignTemp 25
> reassignIncr 25
> reassignHold 310
>
>
> # Minimization
> minimize 100
>
>
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