Re: Periodic cell has become too small for original patch grid!

From: Jeff Wereszczynski (jmweresz_at_mccammon.ucsd.edu)
Date: Fri Apr 02 2010 - 17:05:50 CDT

I have a different approach to fixing this problem. I believe that the
underlying cause of this error is that the system is resizing too quickly
(due to the system pressure being far from the specified pressure). To slow
the resizing down I increase langevinPistonPeriod to 1000 and
langevinPistonDecay to 500 for a short time when I start the NPT simulation,
and then switch to the normal values of 100 and 50.

For example, in your case I would do one input file for 100 ps with a
constraintscaling of 10, langevinPistonPeriod of 1000, and a
langevinPistonDecay of 500. Then I would load the restart files into a new
simulation and proceed as you were above. Also, by restarting the
simulation you are forcing NAMD to re-assign the patches, which will help
prevent this error.

Hope this helps,
Jeff

On Fri, Apr 2, 2010 at 1:36 PM, Philip Peartree <
p.peartree_at_postgrad.manchester.ac.uk> wrote:

> 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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