Re: Polymer moves to the edge of water box during the simulation

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Tue Apr 12 2016 - 17:02:19 CDT

Hi,

My configuration file is as follows:

############################################################
## JOB DESCRIPTION ##
#############################################################

# Equilibration of G5 Alkyne OH terminated
# dendron in a Water Box

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure Alkyne-NPT/Alkyne_OH_wb.psf
coordinates Alkyne-NPT/Alkyne_OH_wb.pdb

set temperature 300
set outputname Al_OH_NPT

# Continuing a job from the restart files
if {1} {
set inputname Al_300_eq ;# only need to edit this
in one place!
binCoordinates $inputname.restart.coor ;# coordinates from last
run (binary)
binVelocities $inputname.restart.vel ;# velocities from last run
(binary) ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.restart.xsc ;# cell dimensions from
last run
}

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters Alkyne-NPT/par_all36_prot.prm
parameters Alkyne-NPT/par_all36_Alkyne.prm

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
# temperature $temperature

# Force-Field Parameters
exclude scaled1-4 ;# These are specified by CHARMM
1-4scaling 1.0 ;# These are specified by CHARMM
cutoff 12.0 ;# may use smaller, maybe 10.0, with PME
switching on
switchdist 10.0 ;# cutoff - 2.0
pairlistdist 14.0 ;# Promise that atom won’t move more than
2A in a cycle, cutoff + 2

# Integrator Parameters
timestep 0.5 ;# 0.5 fs/step
rigidBonds water
nonbondedFreq 1 ;# nonbonded forces every step
fullElectFrequency 2 ;# PME only every other step
stepspercycle 10 ;# redo pairlists every ten steps

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {0} {
cellBasisVector1 49.14 0.00 0.00
cellBasisVector2 0.00 91.77 0.00
cellBasisVector3 0.00 0.00 52.44
cellOrigin -1.97 45.97 1.42
}
wrapWater on ;# wrap water to central cell
wrapAll on ;# wrap other molecules too
wrapNearest off ;# use for non-rectangular cells

# PME (for full-system periodic electrostatics)
if {1} {
PME yes

# let NAMD determine grid
PMEGridSpacing 1.0
}

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 1000 ;# 1000 steps = every 0.5 ps
dcdfreq 500
xstFreq 500
outputEnergies 200
outputPressure 200
outputTiming 1000 ;# shows time per step and time to completion

#############################################################
## EXTRA PARAMETERS ##
#############################################################

margin 5

#############################################################
## EXECUTION SCRIPT ##
#############################################################

run 1200000 ;# 600 ps

and I have one more question. I do not get error just when consider time
step as 0.5 fs. When I set the time step 1.0 fs I get this error
Low global CUDA exclusion count! (13856 vs 13858) System unstable or
pairlistdist or cutoff too small.
Do you think is there any way to prevent this error?

Regards,
Farideh

On Tue, Apr 12, 2016 at 5:54 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Farideh,
>
> Why is this a problem? Things move in simulation. That's kinda the point.
> :D What are your wrapping options? Odds are you have wrap water or wrap all
> turned on, and you are getting thrown because it isn't wrapping like you
> expect.
>
> -Josh
>
>
> On 04/12/2016 04:49 PM, faride badalkhani wrote:
>
> Dear all,
>
> I am performing a NPT simulation for a hyperbranched polymer in water box--089e01160ffeac05bc053050d01b--

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