Membrnae (POPE)/protein simuliation.

From: (
Date: Thu Nov 01 2007 - 07:44:10 CDT

Hi all,
I was trying to equilibrate a protein/lipid system,and the simulation goes well
except some inexplicable (at least I cannot explain it) phenomena.

I first minimize this system, and then I melt the tail (400K). After that I did
the constrained MD (three steps, aim to release the system solwly).Finally, I do
the equilibration MD (10ns). Everythings seems OK! The two leafs of the membrane
is perfect (at least in my mind), however, when I checked the area_per_lipid and
the thickness of the lipid, I met the problem. The area_per_lipid increased from
68 to 74, and the thickness decreased from 38 to 34! Is it normal? To my knowlege,
it's not.

In the equilibration run, I turn the "useconstantarea" on, however I really doubt
this point. Should I turn it on? If yes,when should I turn on? By the way, a
member of our group didn't turn it on during his work and everything is fine.Any
suggeetin will be highly appreciated! Thanks in advance!


P.S. My equilibration MD configuration is below:

structure ./btuc_b12_pope_solvated_modified_ionized.psf
coordinates ./btuc_b12_pope_solvated_modified_ionized.pdb
outputName ../outputs_btuc_b12_pope/btuc_b12_pope_eq1_nogap

bincoordinates ../outputs_btuc_b12_pope/btuc_b12_pope_cons2_nogap.restart.coor
binvelocities ../outputs_btuc_b12_pope/btuc_b12_pope_cons2_nogap.restart.vel
extendedSystem ../outputs_btuc_b12_pope/btuc_b12_pope_cons2_nogap.restart.xsc

set temperature 310
firsttimestep 0

paraTypeCharmm on
parameters ../pars/par_all27_prot_lipid_b12+.inp

wrapWater on
wrapAll on

exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

if {1} {
PME yes
PMEGridSizeX 100
PMEGridSizeY 90

langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea yes ;# no for water box, yes for membrane

if {1} {
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

restartfreq 5000
dcdfreq 5000
xstFreq 5000
outputEnergies 500
outputPressure 500

margin 2.5
run 5000000

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