From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Mon Jul 16 2012 - 15:03:53 CDT
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
>
>
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