From: Philip Peartree (p.peartree_at_postgrad.manchester.ac.uk)
Date: Tue Apr 06 2010 - 09:52:59 CDT
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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