From: snoze pa (snoze.pa_at_gmail.com)
Date: Fri Apr 02 2010 - 13:33:35 CDT
If increase in margin is not helpful then try to translate the center
to PDB file to origin (0,0,0) of the coordinate system. Create new PDB
and PSF files. This helped me a lot many times to avoid margin error
message.
On Thu, Apr 1, 2010 at 8:27 AM, Philip Peartree
<p.peartree_at_postgrad.manchester.ac.uk> wrote:
> Hi All,
>
> I'm getting the above error with one of my simulations, I read the tips
> given on here and have increased the margin (initially 0) to 2.5 and this
> has made no difference. Unfortunately I can't restart at an earlier stage,
> as this is the first step of my equilibration. Below is my input:
>
> #Heating script, change according to correct molecule
>
> # input
> coordinates 2HKM_f_ionized.pdb
> structure 2HKM_f_ionized.psf
> binCoordinates 2HKM_f_therm.coor
> binVelocities 2HKM_f_therm.vel
> parameters par_ttw_namd.inp ;# parameter file for simulation
> paratypecharmm on
> extendedSystem 2HKM_f_therm.xsc
>
>
> # output
> set output 2HKM_f_eq1
> outputname $output
> dcdfile ${output}.dcd
> xstFile ${output}.xst
> dcdfreq 50
> xstFreq 50
>
> binaryoutput yes
> binaryrestart yes
> outputEnergies 100
> outputTiming 50
> restartfreq 1000
>
> # Basic dynamics
>
> exclude scaled1-4
> 1-4scaling 1
> COMmotion no
> dielectric 1.0
> rigidBonds all
>
> # Simulation space partitioning
>
> switching on
> switchdist 12
> cutoff 14
> pairlistdist 16
>
> # Multiple timestepping
>
> firsttimestep 0
> timestep 1
> stepspercycle 20
> nonbondedFreq 2
> fullElectFrequency 4
>
> # PBC (commented out settings not needed with xsc)
>
>
> #cellBasisVector1 82 0 0 ;#set correct basis vectors and origin
> #cellBasisVector2 0 72 0
> #cellBasisVector3 0 0 83
> #cellOrigin 5.11 1.78 0.03
> wrapAll on
> wrapWater on
> dcdUnitCell yes
> useGroupPressure yes
> useFlexibleCell no
> useConstantRatio no
> margin 2.5
>
> #PME
>
> PME on
> PMEGridSpacing 1
>
> #Langevin Settings
>
> langevin on
> langevinTemp 300
> langevinDamping 3.0 # 3 for equilibration 1
> langevinHydrogen off
>
> langevinPiston on
> langevinPistonTarget 1.00 ;# in bar.
> langevinPistonPeriod 100 ;# in fs.
> langevinPistonDecay 50
> langevinPistonTemp 300 ;# set same as langevinTemp.
>
> # Constraints
>
> constraints on
> consRef 2HKM_f_theq_const.pdb
> consKFile 2HKM_f_theq_const.pdb
> consKCol B
> constraintScaling 10
>
>
> run 100000 ; # run for 100 ps
>
> constraintScaling 5
>
> run 100000 ; # run for 100 ps
>
> constraintScaling 2.5
>
> run 100000
>
> constraintScaling 1
>
> run 100000
>
> constraintScaling 0.5
>
> run 100000
>
> Any help would be appreciated, although I will continue to play with things
> until then!
>
> Philip Peartree
> University of Manchester
>
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