Re: Large protein translation during minimization

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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