Re: periodic boundary condition in XY, hard wall in Z - errors

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu Mar 10 2016 - 11:21:00 CST

My system consists of 200 argon atoms in a box, PBC in X and Y, I
would like hard wall in Z and my goal is to measure
density/concentration. So I think that NPT is reasonable in my case,
is that correct?

I commented out PME, because I read that it will speed up
calculations, also because, if I understand it correctly, it requires
all three cell basis vectors to be defined.

linaccel is commented because I defined my own force in a separate
file for the force.

Here is my configuration file:

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

# Equilibration of argon atoms with PBC in XY direction

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

structure ar.psf
coordinates ar.pdb

set temperature 310
set outputname ar_force_out

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters My_parameters.rtf
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# 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

# Periodic Boundary Conditions
cellBasisVector1 62.0 0. 0.0
cellBasisVector2 0.0 62.0 0.0
cellBasisVector3 0.0 0 0.0
cellOrigin 30.0 30.0 32.5

wrapAll on

margin 10

# PME (for full-system periodic electrostatics)
#PME yes
#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

##################
###DEFINE FORCES##
##################

tclForces on
tclForcesScript my_force.tcl
#set linaccel "30 0 0"

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

# Minimization
minimize 100
reinitvels $temperature

run 100000

Thanks!!

Olga

On Thu, Mar 10, 2016 at 2:05 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
> We need to see your full input script, since it looks you're doing npt?
>
> Norman Geist
>
>> -----Ursprüngliche Nachricht-----
>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>> Auftrag von Olya Kravchenko
>> Gesendet: Donnerstag, 10. März 2016 04:23
>> An: NAMD <namd-l_at_ks.uiuc.edu>
>> Betreff: namd-l: periodic boundary condition in XY, hard wall in Z - errors
>>
>> Hi all,
>>
>> I would like to apply periodic boundary conditions only in X and Y
>> directions. In my config file I used the following entry:
>>
>> # Periodic Boundary Conditions
>> cellBasisVector1 70.0 0. 0.0
>> cellBasisVector2 0.0 70.0 0.0
>> cellBasisVector3 0.0 0 0.0
>> cellOrigin 30.0 30.0 32.5
>>
>> wrapAll on
>> margin 5
>>
>>
>> When I submit the job it runs for a while until I see the following error:
>>
>> WRITING COORDINATES TO DCD FILE ar_force_out.dcd AT STEP 20750
>> FATAL ERROR: Periodic cell has become too small for original patch grid!
>> Possible solutions are to restart from a recent checkpoint,
>> increase margin, or disable useFlexibleCell for liquid simulation.
>>
>> How can I address this error? Is this the right way to set up PBC in 2
>> dimensions?
>>
>> My simulation cell is actually around (~61 ~61 ~62), as measured by
>> minmax. I played with numbers and noticed that my simulation runs
>> longer if I increase both the margin and cell basis vectors.
>>
>> I saw some of the older threads in the archives where the margin was
>> discussed but it's not clear how large should it be. If I want to run
>> my simulation for 500 000 steps, what margin should I set up?
>>
>> Also, when choosing cell basis vector, how much bigger should it be
>> than what is measured by "measure minmax"?
>

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