From: khalil ghafarian (khalil_earth_at_yahoo.com)
Date: Tue Oct 09 2012 - 03:40:20 CDT
in PBC, I put empty space as a vacuum beside water box (in x direction), then in SMD section I applied external force in the same direction to my molecule. but as I said the whole water molecules move In X direction along with my molecule!
Here is my config file:
set temperature 298
# input
coordinates input/output-inh-water.restart.coor
extendedSystem input/output-inh-water.restart.xsc
velocities input/output-inh-water.restart.vel
structure input/inh-water.psf
parameters input/inh-water.par
paratypecharmm on
# output
set output output-SMD-inh-water
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 1000
xstFreq 1000
binaryoutput no
binaryrestart no
outputEnergies 100
restartfreq 1000
# Basic dynamics
exclude scaled1-4
1-4scaling 1
COMmotion no
dielectric 1.0
# Simulation space partitioning
switching on
switchdist 10
cutoff 12
pairlistdist 14
#margin 2
# Multiple timestepping
firsttimestep 0
timestep 1
stepspercycle 20
nonbondedFreq 2
fullElectFrequency 4
# Temperature control
#temperature $temperature; # initial temperature
# Langevin Dynamics
langevin on; # do langevin dynamics
langevinDamping 1; # damping coefficient (gamma) of 1/ps
langevinTemp $temperature; # bath temperature
langevinHydrogen no; # don't couple langevin bath to hydrogens
seed 12345
# Pressure control
langevinPiston off
langevinPistonTarget 1.01325; # in bar -> 1.01325 bar = 1 atm
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp $temperature
useFlexibleCell no
useGroupPressure no
fixedAtomsForces off
# PBC
#cellBasisVector1 200 0 0
#cellBasisVector2 0 30 0
#cellBasisVector3 0 0 30
wrapAll on
dcdUnitCell yes
PME yes
PMEGridSpacing 1.0
# SMD SECTION
SMD on
SMDFile input/inh-water.ref
SMDk 50
SMDVel 0.000005
SMDDir 1 0 0
SMDOutputFreq 100
# Scripting
run 9000000
________________________________
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
To: khalil ghafarian <khalil_earth_at_yahoo.com>; "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Sent: Monday, October 8, 2012 3:30 PM
Subject: Re: namd-l: Fixed atoms in SMD
How should it be possible to pull a molecule out of the water, when you have periodic boundaries?
--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
________________________________
From: khalil ghafarian <khalil_earth_at_yahoo.com>
Sender: owner-namd-l_at_ks.uiuc.edu
Date: Mon, 8 Oct 2012 03:22:25 -0700 (PDT)
To: namd-l_at_ks.uiuc.edu<namd-l_at_ks.uiuc.edu>
ReplyTo: khalil ghafarian <khalil_earth_at_yahoo.com>
Subject: namd-l: Fixed atoms in SMD
Hi,
I want to pull out a molecule from water box with SMD, but when I implemented SMD ,I see the whole water box move with my
molecule too , how can I keep water box fixed ?
I have used PBC and I
specified SMD atoms exactly in reference file.
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