From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Sun Nov 04 2007 - 21:25:45 CST
Sorry to add some information, I use 6 Na+ to neutralize the protein -water
system, however, after minimizing the system, these 6 Na+ seems forming
bonds with the TIP3P water. I do not know how to tackle this problem. Shoud
I delete the water involving with Na+. before the MD
On 11/4/07, Shulin Zhuang <shulin.zhuang_at_gmail.com> wrote:
>
> Dear All,
>
> I do equilibration MD simulation of protein in water sphere with NAMD2.6.
> The protein is I27, 89 resiudes,pdb 1tit. I have once sucessfully do 1 ns
> equilibration of I 27. However, when this time, I just delete the last
> residue 89, when I run equilibration at 392 ns, the MD stops and give the
> error information:FATAL ERROR: Bad global exclusion count! How can I tackle
> this problem.
>
> Here, I put my configuration file of equilibration MD. Wish anyone will
> help me out of this problem. Great thanks. Following is the configuration
> file. For this configuration file, I just use it to do 1 ns equlibration of
> I 27 without deleting residue 89.
>
>
> #############################################################
> ## Production run MD run ##
> ## in Water Sphere ##
> #############################################################
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> # molecular system
> set MOL 1tit
> structure ${MOL}_sol_ionize.psf
>
> set outputname ${MOL}_prod
> set prod_restart ${MOL}_prod_restart
>
> # after heating system
> set inprot ${MOL}_heat
> coordinates ${inprot}.coor
> velocities ${inprot}.vel
> extendedSystem ${inprot}.xsc
>
> set temperature 300 ;# initial temperature
>
> # Continuing a job from the restart files
> if {0} {
> set inputname myinput
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel ;# remove the "temperature"
> entry if you use this!
> extendedSystem $inputname.xsc
> }
>
> firsttimestep 0
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters par_all27_prot_lipid_na.inp
>
> # Spherical boundary conditions
> sphericalBC on
> sphericalBCcenter -1.9094337225 0.573376715183 0.0411463677883
> sphericalBCr1 31.2752613824
> sphericalBCk1 10
> sphericalBCexp1 2
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 13.0
> switching on
> switchdist 10.0
> pairlistdist 14.5
>
>
> # Integrator Parameters
> timestep 1.0 ;# 1fs/step
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
> # Constant Temperature Control
> # A: for heating, use temperature reassignment
> if {0} {
> reassignFreq 500 ;# tuned to be suit 'natural' heating for system.
> reassignTemp 25 ;# to start from 0 Kelvin, else always lagging by
> 25K.
> reassignIncr 25
> reassignHold $temperature
> }
>
> # B: for heating, Temperature coupling via Langevin dynamics
> if {1} {
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# couple langevin bath to hydrogens
> }
>
> # Constant Pressure Control (variable volume)
> if {0} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no ;# 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 100
> langevinPistonDecay 50
> langevinPistonTemp $temperature
> }
>
> # for saving restart file
> if {0} {
> restartname $prod_restart
> restartfreq 200 ;# 500steps = every 0.5ps
> restartsave yes
> binaryrestart yes ;# yes will preserves more accuracy.
> }
>
> # Output
> outputName $outputname
> dcdfreq 200
> xstFreq 200
> outputEnergies 100
> outputTiming 100
> binaryoutput yes
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {0} {
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile fix_backbone.pdb
> fixedAtomsCol B
> }
>
> # 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 ##
> #############################################################
>
> # Put here any custom parameters that are specific to
> # this job (e.g., SMD, TclForces, etc...)
>
> #constantforce yes
> #consforcefile ../common/example-output/ubq_ww_eq2.ref
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {0} {
> minimize 3000
> }
>
> run 1000000
> #production for 1ns
>
>
>
>
>
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