protein/lipid simulation

From: Stephen M. Dutz (
Date: Sun Mar 25 2007 - 20:41:23 CDT

Hi all,
I am somewhat new to protein embedded lipid simulations in NAMD. Over the past month I've been attempting to build and simulate a protein embedded in a POPC membrane in NAMD. Unfortunately, I've been unable to obtain a properly equilibrated system to do so. The current build process I'm using is as follows;
(1) Obtain POPC membrane from VMD, remove waters
(2) Graphically place protein in middle of POPC
(3) Use combine.tcl script to obtain pdb/psf
(4) Solvate using "solvate" in VMD, remove any waters from the non-polar side regions
(5) Add counter-ions to neutralize
I then minimize the system (protein unfixed) for 1,000 fs. The system after minimization can be viewed here; . After this, I equilibrate the system (protein fixed), allowing a 10ps 'soak time,' I then restart for an additional 250ps. My problem is that I am unable to obtain a properly equilibrated system. The configuration file I have been using for the equil. soak and restart is as follows (the restart having "run 250000");
# input
structure ../minimize1_2/cff2neutral.psf
coordinates ../minimize1_2/cff2protfix.pdb
bincoordinates ../minimize1_2/cff2_min.coor
extendedSystem ../minimize1_2/cff2_min.xsc
parameters ../../firstrun/gaff.par
parameters ../../firstrun/par_all22_prot.inp
parameters ../../firstrun/par_all27_lipid.prm
paratypecharmm on
# force field parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12
switching On
switchdist 10
pairlistdist 14
rigidBonds all
rigidTolerance 0.00000001
# integrator params
timestep 1
nonbondedFreq 1
PME yes
PMEGridSizeX 55
PMEGridSizeY 55
PMEGridSizeZ 100
fullElectFrequency 4
stepspercycle 20
# temperature
langevin on # do langevin dynamics
langevinDamping 1 # damping coefficient (gamma) of 5/ps
langevinTemp 310.00 # bath temperature
temperature 310
cellBasisVector1 53.842 0 0
cellBasisVector2 0 51.837 0
cellBasisVector3 0 0 99.933
margin 4
wrapAll off
xstFile eq01.xst
xstFreq 1000
# pressure
useConstantArea yes
useFlexibleCell yes
useGroupPressure yes
langevinPiston on
langevinPistonTarget 1.01325 # in bar -> 1 atm
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 310
# output
outputname eq01
restartfreq 500
dcdfreq 500
DCDUnitCell yes
outputEnergies 10
outputTiming 100
binaryoutput no
binaryrestart yes
fixedAtoms on
fixedAtomsCol B
run 10000

After the equilibration run a few problems exist; the most obvious of which is the water seems to continually drift in an upward/outward direction. An image can be viewed here; . I have tried adjusting many parameters; enabling wrapAll (, after 10ps, water not shown) and wrapWater (, after 10ps), both made the system worse; I tried using useConstantRatio rather than useConstantArea, this resulted in the lipid continually expanding outward. Additionally, I tried minimizing for 10,000 fs, this did not improve matters. I've looked at past posts to the mailing list and have tried some of the recommendations I have seen, however nothing seems to do the trick. Any insight would be greatly appreciated.
Thank You,

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