From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Jul 16 2012 - 16:59:22 CDT
Yeah, I would think you could apply the periodic conditions just as you
say. I've never tried it without PME, but they are separate flags so I
don't see a problem.
On Mon, Jul 16, 2012 at 5:43 PM, Roy Fernando <roy.nandos_at_gmail.com> wrote:
> Thanks for the great details Aron. Axel,Ajasja
>
> I understand things better now.
>
> I got a question here. Is it all right to apply periodic boundary
> conditions within GBIS method. I still think that means giving the beriodic
> cell size only. Not specifying PME cell sizes?
>
> It is always great share problems with NAMD community.
>
> Roy
>
>
> On Mon, Jul 16, 2012 at 5:27 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>
>> yeah, as Axel says, it suggests that your atoms flew apart in the
>> simulation to the extend that there coordinates got so large they could no
>> longer be written. I guess you have various options
>>
>> 1) as Ajasja says, you could make a periodic boundary for your system in
>> order to trap everything.
>>
>> 2) drop the temperature considerably, or, if you are particular about the
>> temperature, drop the timestep considerably (go for 0.1 or something
>> instead of 2.0).
>>
>> 3) look at the starting coordinates carefully and make sure there isn't
>> some kind of atomic overlap that would have sent the atoms flying away from
>> one another.
>>
>> 4) To expand on what Axel said about forces, I would reconsider some of
>> your parameters, particularly "cutoff 4.0". Since your whole system is
>> non-bonded, it means that once your neons are > 4.0 angstroms from one
>> another, there are no longer any forces calculated, and they will just
>> fly. Even for an explicit solvent system you'd want that to be at least
>> 10.0, and for implicit solvent, likely higher (since you can't use PME).
>> For your case, you are only simulating two atoms, so you really shouldn't
>> even use a cutoff. I would set it to 999, and turn off switching.
>>
>> ~Aron
>>
>>
>>
>> On Mon, Jul 16, 2012 at 4:46 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>>
>>> NaN means "not a number" which means, that
>>> your input is bonkers and that your forces may
>>> be way off the chart.
>>>
>>> axel.
>>>
>>> On Mon, Jul 16, 2012 at 10:03 PM, Roy Fernando <roy.nandos_at_gmail.com>
>>> wrote:
>>> > Hi Aron,
>>> >
>>> > I did not try to open the binary file. But I loaded the dcd file on to
>>> the
>>> > psf file in VMD. But I could not see anything.
>>> > Also, I tried to take simple measurements for the system such as
>>> measure
>>> > minmax. I got the results {-NaN -NaN -NaN} {-NaN -NaN -NaN}
>>> >
>>> > Also I tried to write a pdb file for the very first and last frames of
>>> the
>>> > simulation but it failed. I got the following message.
>>> > atomsel: writepdb failed.
>>> >
>>> > However, I could run a TCl force simulation without equilibrating the
>>> > system. I could write pdb files for the frames of this simulation.
>>> >
>>> > do you have any suggestions for me?
>>> >
>>> > Regards,
>>> >
>>> > Roy
>>> >
>>> >
>>> >
>>> > On Sun, Jul 15, 2012 at 9:31 PM, Aron Broom <broomsday_at_gmail.com>
>>> wrote:
>>> >>
>>> >> what do you mean by missing? Do you mean that if you open up the
>>> output
>>> >> NE2_gbis_eq.coor file, the file is empty?
>>> >>
>>> >>
>>> >> On Sun, Jul 15, 2012 at 6:13 PM, Roy Fernando <roy.nandos_at_gmail.com>
>>> >> wrote:
>>> >>>
>>> >>> Dear All,
>>> >>>
>>> >>> I try to simulate my test system containing two Neon atom under
>>> >>> Generalized Born Implicit Solvent Technique.
>>> >>> I did not use any charge.
>>> >>> At the end of the equilibration, I observe that the atoms are
>>> missing.
>>> >>> I used the basic configuration file came with the tutorial. (posted
>>> >>> below).
>>> >>> I will appreciate if someone can give some insight on how I can keep
>>> the
>>> >>> atoms confined to a certain volume. Or is it not possible in this
>>> method?
>>> >>>
>>> >>> regards,
>>> >>>
>>> >>> Roy
>>> >>>
>>> >>> #############################################################
>>> >>> ## JOB DESCRIPTION ##
>>> >>> #############################################################
>>> >>>
>>> >>> # Minimization and Equilibration of
>>> >>> #Neon atoms in generalized Born implicit solvent
>>> >>>
>>> >>>
>>> >>> #############################################################
>>> >>> ## ADJUSTABLE PARAMETERS ##
>>> >>> #############################################################
>>> >>>
>>> >>> structure NE2-1.psf
>>> >>> coordinates NE2-1.pdb
>>> >>>
>>> >>> set temperature 310
>>> >>> set outputname NE2_gbis_eq
>>> >>>
>>> >>> firsttimestep 0
>>> >>>
>>> >>>
>>> >>> #############################################################
>>> >>> ## SIMULATION PARAMETERS ##
>>> >>> #############################################################
>>> >>>
>>> >>> # Input
>>> >>> paraTypeCharmm on
>>> >>> parameters par_all27_prot_lipid.inp
>>> >>> temperature $temperature
>>> >>>
>>> >>> # Implicit Solvent
>>> >>> gbis on
>>> >>> alphaCutoff 2.0
>>> >>> ionConcentration 0.0
>>> >>>
>>> >>> # Force-Field Parameters
>>> >>> exclude scaled1-4
>>> >>> 1-4scaling 1.0
>>> >>> cutoff 4.0
>>> >>> switching on
>>> >>> switchdist 3.0
>>> >>> pairlistdist 6.0
>>> >>>
>>> >>>
>>> >>> # Integrator Parameters
>>> >>> timestep 2.0 ;# 2fs/step
>>> >>> rigidBonds all ;# needed for 2fs steps
>>> >>> nonbondedFreq 1
>>> >>> fullElectFrequency 2
>>> >>> stepspercycle 10
>>> >>>
>>> >>>
>>> >>> # Constant Temperature Control
>>> >>> langevin on ;# do langevin dynamics
>>> >>> langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
>>> >>> langevinTemp $temperature
>>> >>> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>>> >>>
>>> >>> # Output
>>> >>> outputName $outputname
>>> >>>
>>> >>> restartfreq 500 ;# 500steps = every 1ps
>>> >>> dcdfreq 250
>>> >>> xstFreq 250
>>> >>> outputEnergies 100
>>> >>> outputPressure 100
>>> >>>
>>> >>>
>>> >>> #############################################################
>>> >>> ## EXTRA PARAMETERS ##
>>> >>> #############################################################
>>> >>>
>>> >>>
>>> >>> #############################################################
>>> >>> ## EXECUTION SCRIPT ##
>>> >>> #############################################################
>>> >>>
>>> >>> # Minimization
>>> >>> minimize 1000
>>> >>> reinitvels $temperature
>>> >>>
>>> >>> run 25000 ;# 5ps
>>> >>>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> Aron Broom M.Sc
>>> >> PhD Student
>>> >> Department of Chemistry
>>> >> University of Waterloo
>>> >>
>>> >
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>>
>>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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