From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 01 2014 - 07:48:34 CDT
On Mon, Sep 1, 2014 at 2:33 PM, Siva Dasetty <sdasett_at_g.clemson.edu> wrote:
> Hello,
>
> Thank you for the reply. There is nothing else in the system, its just
> graphene (1 and 2 layered) in implicit solvent. This is just a test case I
> am running as I am very new to NAMD. Below is the configuration file I have
> used, Kindly please let me know your suggestions.
if nothing can move, what are you trying to optimize then?
and to paraphrase my previous question (which you only answered in an
extremely vague fashion):
how can you compute a temperature, when you have 0 DOFs?
axel.
>
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Minimization and Equilibration of
> # Graphene in generalized Born implicit solvent
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure gra_sheet.psf
> coordinates gra.pdb
>
> set temperature 0
> set outputname eq_gra
>
> firsttimestep 0
> vdwGeometricSigma yes
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters par_gra.inp
> temperature $temperature
>
> #Timestep Parameters
> timestep 2.0 ;# 2fs/step
> numsteps 5000 ;#number of simulation timesteps
> nonbondedFreq 1
> fullElectFrequency 2
>
> # Implicit Solvent Parameters
> gbis on
> alphaCutoff 15.0
> GBISDelta 1
> GBISBeta 0.8
> GBISGamma 4.85
>
>
> # Force-Field Parametiers
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 15.0
> switching on
> switchdist 10.0
> pairlistdist 16.0
> #Fixed atom parameters
> fixedAtoms on
> #fixedAtomsForces on
> #fixedAtomsFile new.pdb
> #fixedAtomsCol B
> #rigidBonds all
>
> # 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 2000 ;# 2000steps = every 4ps
> dcdfreq 2500
> xstFreq 2500
> outputEnergies 2500
> outputPressure 2500
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 100
>
>
>
>
>
>
>
>
>
> Thanks,
> Siva
>
>
> On Mon, Sep 1, 2014 at 3:26 AM, Norman Geist
> <norman.geist_at_uni-greifswald.de> wrote:
>>
>>
>>
>> > -----Ursprüngliche Nachricht-----
>> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>> > Auftrag von Siva Dasetty
>> > Gesendet: Samstag, 30. August 2014 03:12
>> > An: namd-l_at_ks.uiuc.edu
>> > Betreff: namd-l: Fixing atoms while equilibration
>> >
>>
>> > Dear All,
>> >
>> > I am doing an energy minimization of graphene in implicit solvent by
>> > fixing all graphene atoms using fixedAtoms=on in NAMD version 2.10b1.
>> > As expected all the energies are 0 in my output log file as I excluded
>> > all bonded and non bonded interactions, however temp and tempavg seems
>> > to have this huge number “999999999.99999”. Can someone please explain
>> > this?
>>
>> Hi,
>>
>> as the minimizer works at zero Kelvin and you have temperature, I think
>> you
>> did something wrong with your script.
>> Also, what else is in your system in order to be minimized if you graphene
>> is fixed?
>>
>> Norman Geist
>>
>> >
>> > Thanks,
>> > Siva
>>
>>
>> ---
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>>
>
>
>
> --
> Siva Dasetty
> PhD Student
> Department of Chemical and Biomolecular Engineering
> Clemson University
> Clemson, SC 29634
> USA
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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