From: Philip Peartree (p.peartree_at_postgrad.manchester.ac.uk)
Date: Tue Apr 06 2010 - 16:19:15 CDT
I will calculate the density to check, but the main problem with trying to
bootstrap as you put it, is that it dies with that error at step 1, so I
have no prior configurations to run from... I suspect it might be my
constraints, which are actually holding the system in a state which it
doesn't want to be in... so I'm relaxing these off whilst running with the
1000/500 period/decay setting and then I'm going to try running with the
100/50 and see where I get with that.
Philip Peartree
University of Manchester
On 6 April 2010 17:18, Jeffrey J. Potoff <jpotoff_at_chem1.eng.wayne.edu>wrote:
> Hi Philip,
> This bottom line is that your system is too far away, in terms of
> density, from where it wants to go. If you have not done so already, you
> should calculate the density of your system and make sure you have enough
> water to get you to ~1.0g/cm^3.
> If the density seems ok, then you just need to bootstrap off of your first
> simulation. Run until NAMD spits the patch grid error, then use the final
> configuration to feed into your next simulation. After a couple iterations
> you should have a relatively stable density, which will allow you to run
> long simulations without worry of the patch grid error.
> I advise against tinkering with the margin, as in most cases you are
> masking the real problem and making your simulations (potentially) run
> slower.
>
> FYI, The "patch grid error" has been discussed many times on this mailing
> list and you should be able to find nearly every possible "solution" by
> searching the mailing list archives.
> Regards,
> J.
>
> Philip Peartree wrote:
>
>> I tried this, I managed to get 100 ps out of it with the pistonperiod and
>> decay as below. I then tried to revert to 100 and 50 and this gave periodic
>> cell has become too small errors again, so I tried a less drastic stepsize
>> of 500 and 250, the same error. I tried 750 and 375 and got another 100 ps
>> out of it, but again it failed when I reverted to 500 and 250. Anyone got
>> any ideas why this might happen?
>>
>> Also, is there a difference between using the .restart.coor and the normal
>> .coor files?
>>
>> Philip Peartree
>> University of Manchester
>>
>> On 3 April 2010 00:06, Philip Peartree <
>> p.peartree_at_postgrad.manchester.ac.uk <mailto:
>> p.peartree_at_postgrad.manchester.ac.uk>> wrote:
>>
>> That seems like a good idea, I will try that if my re-min doesn't
>> solve the problem!
>>
>>
>> On 2 April 2010 23:05, Jeff Wereszczynski
>> <jmweresz_at_mccammon.ucsd.edu <mailto:jmweresz_at_mccammon.ucsd.edu>>
>>
>> wrote:
>>
>> 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
>> <mailto: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
>> <http://snoze.pa>@gmail.com <http://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
>> <mailto: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
>> >
>>
>>
>>
>>
>>
>>
>
> --
> ======================================================================
> Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
> Associate Professor Wayne State University
>
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
> ======================================================================
>
>
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