RE: About Columb energy of 2 ions in Vacuum

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Aug 26 2011 - 01:37:05 CDT

The switching distance applies to the vdW forces only. When switching is
on, electrostatic forces get rescaled all the way from zero to the cutoff.
See the plots here: http://www.ks.uiuc.edu/Research/namd/2.8/ug/node24.html

I also found a really old NAMD webpage that describes the exact functions
used for scaling the interactions:
http://www.ks.uiuc.edu/Research/namd/1.5/ug/node52.html

I hope this clarifies the issue. I remember (re)discovering the same thing
a few years ago.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of wenhao_at_uchicago.edu
Sent: Thursday, August 25, 2011 6:02 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: About Columb energy of 2 ions in Vacuum

Hi,

The system is 2 ions in Vacuum, I fixed 2 ions with a 8 angstrom, my config
files is as following:
###################################################
# EQUILIBRATION
###################################################

# INPUT

set temp 0.0

parameters par_all22_prot.inp
paraTypeCharmm on

exclude scaled1-4
1-4scaling 1.0

# TOPOLOGY

structure 2ions_autopsf.psf

# INITIAL CONDITIONS

coordinates 2ions_autopsf.pdb
temperature $temp

# OUTPUT FREQUENCIES

outputenergies 1
outputtiming 1
outputpressure 1
restartfreq 1
XSTFreq 1
dcdfreq 500

# OUTPUT AND RESTART

outputname equil
restartname equil

binaryoutput yes
binaryrestart yes

# PME
# PME no
# PMEPencils 16
# PMETolerance 1.0e-6
# PMEInterpOrder 6
# PMEGridSpacing 1.0

# PME no
#PMETolerance 10e-6
#PMEInterpOrder 4
#PMEGridSpacing 1.0

# Periodic Boundary Conditions
cellBasisVector1 30.0 0.0 0.0
cellBasisVector2 0.0 30.0 0.0
cellBasisVector3 0.0 0.0 30.0
cellOrigin 0.0 0.0 0.0

# WRAP WATER FOR OUTPUT

#wrapAll on

# CONSTANT-T
#langevin on
#langevinTemp $temp
#langevinDamping 1.0

# CONSTANT-P

# LangevinPiston on
# LangevinPistonTarget 1
# LangevinPistonPeriod 100
# LangevinPistonDecay 100
# LangevinPistonTemp $temp

#StrainRate 0.0 0.0 0.0
#useGroupPressure yes

#useflexiblecell no

# CUT-OFFS

switching on
switchdist 16.0
cutoff 17.0
pairlistdist 18.0

# RESPA PROPAGATOR

timestep 1.0

fullElectFrequency 1
nonbondedFreq 1

#-------------------Fixed
parameters---------------------------------------------------
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile 2ions_autopsf_restrain.pdb
fixedAtomsCol B

run 20
#############################################################

I just to see the log file, due to the formula of Columb energy and the
distance, elect should be equal to 41.5 whereas this will give us a
25kcal/mol. The cutoff is sure larger than the distance so the interaction
should be included in elect. Whether I use PME or not, and also whether I
commen out the periodic boundary condition, I can not get the exact number
of Columb energy.
But if I turn off the switch function, I can get the exact 41.5kcal/mol. So
the switch should be trun off so as to calculate the Columb energy ?

Thanks.
Wenhao

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