Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration

From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Mon Jul 16 2012 - 16:43:04 CDT

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
>
>

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