Membrnae (POPE)/protein simuliation.

From: (ebullience_at_emails.bjut.edu.cn)
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!

Respectfully,
Ming

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
PMEGridSi
}

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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