From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jul 16 2012 - 15:46:51 CDT
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.
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