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【求助】Melting of Lipid Tails后脂雙層有的地方分離 已有2人參與
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Melting of Lipid Tails后脂雙層有的地方分離 這是我的conf文件： ## JOB DESCRIPTION ## ############################################################# # Min. and Eq. of Aqp1 # embedded in POPE membrane, water. # Melting lipid tails. PME, Constant Volume. ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ../02-MEMBRANE/aqp1_popew.psf coordinates ../02-MEMBRANE/aqp1_popew.pdb outputName aqp1_popewmineq-01 set temperature 300 # Continuing a job from the restart files if {0} { set inputname aqp1-popew binCoordinates $inputname.restart.coor binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this! extendedSystem $inputname.restart.xsc } firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../par_all27_prot_lipid.prm # NOTE: Do not set the initial velocity temperature if you # have also specified a .vel restart file! temperature $temperature # Periodic Boundary Conditions # NOTE: Do not set the periodic cell basis if you have also # specified an .xsc restart file! if {1} { cellBasisVector1 105. 0. 0. cellBasisVector2 0. 105. 0. cellBasisVector3 0. 0. 73. cellOrigin -0.077429056167 0.074017807841 -0.44251784668 } wrapWater on wrapAll on # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 20 #PME (for full-system periodic electrostatics) if {1} { PME yes PMEGridSizeX 106 PMEGridSizeY 106 PMEGridSizeZ 74 } # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 1 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature # Constant Pressure Control (variable volume) if {0} { useGroupPressure yes ;# needed for 2fs steps useFlexibleCell yes ;# no for water box, yes for membrane useConstantArea no ;# no for water box, yes for membrane langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 200. langevinPistonDecay 50. langevinPistonTemp $temperature } restartfreq 1000 ;# 1000steps = every 2ps dcdfreq 1000 xstFreq 1000 outputEnergies 50 outputPressure 50 # Fixed Atoms Constraint (set PDB beta-column to 1) if {1} { fixedAtoms on fixedAtomsFile ../02-MEMBRANE/myfixatomfile.pdb fixedAtomsCol B fixedAtomsForces on } ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Put here any custom parameters that are specific to # this job (e.g., SMD, TclForces, etc...) ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization if {1} { minimize 10000 reinitvels $temperature } run 500000 ;# 0.5 ns |
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3樓2011-03-18 22:57:40
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zh1987hs(金幣+3): 鼓勵思考 2011-03-20 22:50:09
zh1987hs(金幣+3): 鼓勵思考 2011-03-20 22:50:09
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這個問題算是暫時解決了，運行后看看吧： 1. 打開壓力 2. 在運行Melting of Lipid Tails前，應(yīng)執(zhí)行： set sel [atomselect top "protein and backbone"] set all [atomselect top all] $all set beta 0 $sel set beta 1 $all writepdb myfixatomfile.pdb 產(chǎn)生的myfixatomfile.pdb放在conf文件fixedAtomsFile 后面 [ Last edited by nufang19a on 2011-3-19 at 22:56 ] |
6樓2011-03-19 21:30:33
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