Large protein translation during minimization

From: Rachel Ruskin (rsrusk_at_gmail.com)
Date: Mon Feb 15 2010 - 16:24:20 CST

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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