**From:** Olya Kravchenko (*ovkrav_at_gmail.com*)

**Date:** Thu Mar 10 2016 - 20:01:12 CST

**Next message:**faride badalkhani: "Urey-Bradley parameters"**Previous message:**Josh Vermaas: "Re: problem with bringing down the pressure"**In reply to:**Maxim Belkin: "Re: periodic boundary condition in XY, hard wall in Z - errors"**Next in thread:**Maxim Belkin: "Re: periodic boundary condition in XY, hard wall in Z - errors"**Reply:**Maxim Belkin: "Re: periodic boundary condition in XY, hard wall in Z - errors"**Reply:**Maxim Belkin: "Re: periodic boundary condition in XY, hard wall in Z - errors"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Thank you! I will study MSM method.

I have changed the size of cell vectors back to 62, that is the actual

size rounded up, and I commented out cellBasisVector3. I ran a number

of simulations today and I keep seeing the same error when I increase

the number of timesteps. The margin size does seem to make the job run

longer, at least I don't see any other correlation. My last run quit

near 150 000 timesteps (I set it up for 500K timesteps).

Apart from that, I see in vmd that my simulation box actually becomes

longer in Z-direction, it is a cube in the beginning and then the

proportion changes. I am not sure how to interpret it, but it looks

like the size in z does not hold, certainly no hard wall. I wonder if

there is a way to set up the hard wall in a simple way?

Olga

On Thu, Mar 10, 2016 at 4:58 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

*> Olya,
*

*>
*

*> If your system size is 60A in x and y, you should use vectors of length 60 as your "cellbasisvector[1,2]". You are currently using 70, which means you have vacuum in x and y directions and this is not what you want. To simulate a system that is non-periodic along Z with NAMD you have to use Multi-level summation method (look for MSM option in NAMD User’s Guide). I believe you have to remove "cellbasisvector3" instead of specifying 0 0 0 but I’m not 100% positive on that.
*

*>
*

*> Maxim
*

*>
*

*>
*

*>> On Mar 10, 2016, at 11:21, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
*

*>>
*

*>> 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"?
*

*>>>
*

*>
*

**Next message:**faride badalkhani: "Urey-Bradley parameters"**Previous message:**Josh Vermaas: "Re: problem with bringing down the pressure"**In reply to:**Maxim Belkin: "Re: periodic boundary condition in XY, hard wall in Z - errors"**Next in thread:**Maxim Belkin: "Re: periodic boundary condition in XY, hard wall in Z - errors"**Reply:**Maxim Belkin: "Re: periodic boundary condition in XY, hard wall in Z - errors"**Reply:**Maxim Belkin: "Re: periodic boundary condition in XY, hard wall in Z - errors"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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