Re: Fixing atoms while equilibration

From: Siva Dasetty (sdasett_at_g.clemson.edu)
Date: Mon Sep 01 2014 - 08:07:59 CDT

Dr.Kohlmeyer,

Thank you again for the reply.
I understand that the DOF=0 and so are the velocities as the atoms are
fixed. Temperature is calculated from K.E (which is calculated by the atoms
velocities) and DOF(0 in this case) using (T = Sum_i (m(i)*v(i)^2) /
(n_DOF*k_B) ).
Yes you cannot compute temperature and this is why I was confused initially
when I saw this huge number 9999999.99 but now it somewhat makes sense as
both numerator and denominator are zeros.
So, does that mean this value I am seeing is equal to infinity in NAMD?

Thanks,
Siva

On Mon, Sep 1, 2014 at 8:48 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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
> >>
> >>
> >> ---
> >> Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus
> >> Schutz ist aktiv.
> >> http://www.avast.com
> >>
> >
> >
> >
> > --
> > 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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