From: Philip Peartree (p.peartree_at_postgrad.manchester.ac.uk)
Date: Tue Apr 06 2010 - 17:56:17 CDT
I've calculated the density by counting the number of water molecules in my
solvation box and doing the usual maths I get a density of around 0.79
g/cm3, which I know is wildly out. My main confusions are:
a) I made the waterbox using vmd's solvate plugin, using molecule
dimensions, boundary of 2.4 and a padding of 12 angstoms all round... are
these settings incorrect? I also left crystal waters in the original psf,
could this have thrown the solvate plugin out?
b) My volume seems to have pretty much stablised and my gpressave is
oscillating around 1 bar (where it is set). Shouldn't the box be getting
smaller to increase density and shouldn't the pressure be too low if the
density is too low as well?
Appologies for the constant questions, I have done quite a few namd
simulations, and I've never experienced this before, or at least not this
difficult to get rid off!!
Philip
On 6 April 2010 22:19, Philip Peartree <p.peartree_at_postgrad.manchester.ac.uk
> wrote:
> 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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