From: Philip Peartree (p.peartree_at_postgrad.manchester.ac.uk)
Date: Fri Apr 02 2010 - 15:36:54 CDT
Any idea how best to do this? If it's any help, I got round this problem
with a margin of 5 but then got a pile of rattle errors, so I figured it was
something wrong with my structure, so I'm re-minimizing them for a longer
number of steps, to see if that helps!
On 2 April 2010 19:33, snoze pa <snoze.pa_at_gmail.com> wrote:
> 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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