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gn02530640銀蟲(chóng) (小有名氣)
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[求助]
NAMD的conf文件，關(guān)于 NVE 和 NVT ensemble 的設(shè)定差別?
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以下2個(gè)conf 文件，一個(gè)是教程里本身包含的 NVE conf 文件，一個(gè)是在網(wǎng)絡(luò)上找到的 NVT conf文件，自己我比對(duì)后實(shí)在看不出有什么差異，有了解NAMD的蟲(chóng)友能說(shuō)明一下嗎? 非常感謝 ubq-nve.conf ############################################################# ## JOB DESCRIPTION ## ############################################################# # Equilibration of Ubiquitin in a Water Sphere # Use for calculating temperature fluctuations # WARNING: DOES NOT SAVE DCD (and normally you need it) ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ../common/ubq_ws.psf coordinates ../common/ubq_ws.pdb set temperature 310 set outputname ubq-nve # Continuing a job from the restart files if {1} { set inputname ../1-2-sphere/ubq_ws_eq 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 ../common/par_all27_prot_lipid.inp #temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 13.5 # Integrator Parameters timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 # Constant Temperature Control if { 0 } { langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens } # Output outputName $outputname #restartfreq 50 ;# 500steps = every 1ps #dcdfreq 50 outputEnergies 50 outputPressure 50 ############################################################# ## EXTRA PARAMETERS ## ############################################################# # Spherical boundary conditions sphericalBC on sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423 sphericalBCr1 26.0 sphericalBCk1 10 sphericalBCexp1 2 ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization # minimize 100 # reinitvels $temperature run 500000 ;# 1000ps NVT.conf !if you set up a simulation with langevin dynamics but without pressure !controls, it will be in the NVT ensemble. For example, the following is !a modification of the ubiquitin equilibration file from the namd !tutorial to be in the NVT ensemble: ############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization and Equilibration of # Ubiquitin in a Water Box ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# structure ../common/ubq_wb.psf coordinates ../common/ubq_wb.pdb set temperature 310 set outputname ubq_wb_eq firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input paraTypeCharmm on parameters ../common/par_all27_prot_lipid.inp temperature $temperature # 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 10 # Constant Temperature Control langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp $temperature langevinHydrogen off ;# don't couple langevin bath to hydrogens # Periodic Boundary Conditions cellBasisVector1 42. 0. 0. cellBasisVector2 0. 44. 0. cellBasisVector3 0. 0 47. cellOrigin 31. 29. 17.5 wrapAll on # PME (for full-system periodic electrostatics) PME yes PMEGridSizeX 32 PMEGridSizeY 32 PMEGridSizeZ 32 useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no useConstantArea no #Note the lack of langevinpiston, which is the pressure control # Output outputName $outputname restartfreq 500 ;# 500steps = every 1ps dcdfreq 250 xstFreq 250 outputEnergies 100 outputPressure 100 ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization minimize 100 reinitvels $temperature run 2500 ;# 5ps |
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