From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jul 13 2011 - 10:54:10 CDT
Try pbc wrap -compound residue -centersel protein, it won't break water
molecules.
Also, try emailing vmd-l next time.
On Wed, Jul 13, 2011 at 11:48 AM, bharat gupta <bharat.85.monu_at_gmail.com>wrote:
> Hi,
>
> I have asked this question previously also . I have repeated the
> equilibration again , but still the protein moves out of the box.
>
> here is the configuration file that I used for minimization and npt
> equilibration :-
>
> Minimization
> ===========
> numsteps 100000
> minimization on
> dielectric 1.0
> coordinates ./ionized.pdb
> outputname complex_min
> outputEnergies 1000
> binaryoutput no
> DCDFreq 1000
> restartFreq 1000
> structure ./ionized.psf
> paraTypeCharmm on
> parameters ../common/par_all27_prot_na.prm
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 8.0
> cutoff 12.0
> pairlistdist 13.5
> margin 0.0
> stepspercycle 10
>
>
>
>
> ===============================
>
> npt equilibration
> ------------------------
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
> # Minimization and Equilibration of
> #GFP in a Water Box
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
> structure ./ionized.psf
> coordinates ./ionized.pdb
> set temperature 310
> set outputname complex_eq
> firsttimestep 0
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
> # Input
> binCoordinates ./complex_min.restart.coor
> binaryrestart yes
> extendedSystem ./complex_min.restart.xsc
> paraTypeCharmm on
> parameters ../common/par_all27_prot_na.prm
> temperature $temperature
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
> margin 2.5
> # 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 65. 0. 0.
> cellBasisVector2 0. 53. 0.
> cellBasisVector3 0. 0 49.
> cellOrigin 0. 0. 0.
> wrapAll on
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 60
> PMEGridSizeY 60
> PMEGridSizeZ 60
> 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 ##
> #############################################################
>
> numsteps 30000
>
>
> I tried using pbc wrap by using the command pbc wrap -centersel protein but
> whole of the box and protein comes out in the form of lines...
>
> Pls help as I am not able to move on with my experiment
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010_at_yahoo.com
>
>
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