Namd-1: problems using increment of temperature during simulation

From: Ye Yang (knightyangpku_at_gmail.com)
Date: Sun Feb 27 2011 - 14:27:16 CST

>
> Hi,
> I am a new user of Namd. When I use temperature
> reassignment/temperature increment, I met some problems:
> I am trying to heat up the protein in the waterbox to see its
> unfolding by temperature increment from 310K.
> It seems to be that I cannot use Langevin dynamics in this way, since
> it is at constant temperature: When I use it, the temperature just do not
> increase, and it does not unfold.
> So I deleted the Langevin dynamics in the configuration file.
> However, when I did this, and extend the simulation time, I found the
> protein just moved out of the water box even before the first heating up
> step(translational movement). Also, the temperature is around 180K, which is
> very wield. Is there any way to solve this problem(I used wrap water, maybe
> wrap all this time)? Or is there any possibility to use Langevin dynamics
> while increasing the temperature?
> Thank you very much.
>
> Ye
>
> Mechanical Engineering
> Duke University
>
>
> The config file goes as follows:
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Equilibration of ConAnk-mut structure
> #
> # EQ NI3C-mut H85R
> # 031110
> # NI3C-mut85-smd.ref
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure NI3C_wb.psf
> coordinates NI3C_wb.pdb
>
> set temperature 310
> set outputname Ni3C
>
> # Continuing a job from the restart files
> if {0} {
> set inputname Mineq-G2a
> BinCoordinates $inputname.restart.coor
> #BinVelocities $inputname.restart.vel ;# remove the "temperature"
> entry if you use this!
> ExtendedSystem $inputname.xsc
> firsttimestep 0
> } else {
> firsttimestep 0
> }
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> temperature $temperature
>
> # Periodic Boundary conditions
> if {1} {
> cellBasisVector1 101.1 0. 0.
> cellBasisVector2 0. 95.76 0.
> cellBasisVector3 0. 0 109.2
> cellOrigin 8.31 23.26 1.27
> }
>
> wrapWater on
> wrapAll off
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 1.0 ;# 1fs/step
> #rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
>
> #PME (for full-system periodic electrostatics, choose prime multiples)
> if {1} {
> PME yes
> PMEGridSizeX 120 ; #2*2*5*5
> PMEGridSizeY 100 ; #
> PMEGridSizeZ 120 ;#
> PMEpencils 1
> }
>
>
> # Constant Temperature Control
> #if {1}
> #{
> #langevin on ;# do langevin dynamics
> #langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> #langevinTemp $temperature
> #langevinHydrogen no ;# don't couple langevin bath to hydrogens
> #}
>
>
> # Constant Pressure Control (variable volume)
> if {1} {
> useGroupPressure no ;# needed for 2fs steps
> useFlexibleCell no ;# x-y-z flexible
> useConstantArea no ;# fix x-y plane, z in motion
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
> }
>
>
> # Output
> outputName $outputname
> restartname $outputname.restart
> dcdfile $outputname.dcd
> xstFile $outputname.xst
> velDCDfile $outputname.vel.dcd
>
> restartfreq 20000 ;# 20000steps = every 20ps
> dcdfreq 5000
> xstFreq 1000
> velDCDFreq 1000
> outputEnergies 1000
> outputPressure 1000
>
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {0} {
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile NI3C-mut85-smd.ref
> fixedAtomsCol B
> }
>
> # Fixed Atoms Constraint (alternate method, Beta column = spr constant k)
> if {0} {
> constraints on
> consKCol B
> consref GB1fibr2a_wb-fixed.pdb
> consKFile GB1fibr2a_wb-fixed.pdb
> }
>
> # Hydrogen Bond Constraints
> if {0} {
> freeEnergy On
> freeEnergyConfig Hbondconstr6.namd
> }
>
> # IMD Settings (can view sim in VMD)
> if {0} {
> IMDon on
> IMDport 3000 ;# port number (enter it in VMD)
> IMDfreq 1 ;# send every 1 frame
> IMDwait no ;# wait for VMD to connect before running?
> }
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
> # Add this part
> # Put here any custom parameters that are specific to
> # this job (e.g., SMD, TclForces, etc...)
> #temperature reassign
> reassignFreq 2000000 ;#2ns
> reassignIncr 10
> reassignHold 374
>
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
>
> if {1} {
> minimize 50000
> reinitvels $temperature
> }
> run 20000000 ;
>

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