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

From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Apr 06 2010 - 10:26:09 CDT

Still you can try my suggestions.. I don't know the logic but it
worked in most of my cases. Transform the PDB center to Origin(0,0,0)
and then create a new psf file. Run namd using margin =4.

On Tue, Apr 6, 2010 at 9:52 AM, Philip Peartree
<p.peartree_at_postgrad.manchester.ac.uk> 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> 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>
>> 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> 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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