POPE/protein simuliation.

From: Ming (ebullience_at_emails.bjut.edu.cn)
Date: Thu Nov 01 2007 - 20:06:37 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
 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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