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
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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