From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Thu Mar 10 2016 - 15:58:45 CST
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"?
>>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:13 CST