From: Philip Peartree (p.peartree_at_postgrad.manchester.ac.uk)
Date: Fri Apr 02 2010 - 18:06:43 CDT
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
>>> >
>>>
>>>
>>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:58 CST