Re: Fixing atoms while equilibration

From: Siva Dasetty (sdasett_at_g.clemson.edu)
Date: Mon Sep 01 2014 - 07:33:57 CDT

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.

#############################################################
## 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

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