From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Fri Mar 11 2016 - 15:31:50 CST
Olya,
NAMD config script below has "langevin on", so this is NPT. Again, NPT simulations are used to equilibrate pressure, usually to 1 atm, which is also what you have set in your script. Vacuum has 0 atm. I have hard time imagining what langevinPiston should do in such a case.
Here is a useful message on the subject:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/4142.html
Maxim
> On Mar 11, 2016, at 14:57, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>
> Maxim,
>
> thank you for replying. I am trying to figure out MSM right now and
> see if it makes difference, I'll try setting exact values for
> cellbasisvectors too.
>
> As for the hard wall: I expected to see expansion in the beginning
> that does not change further, as it happens when I use PBC in 3D. What
> I saw is oscillating continuous expansion, i.e. a couple of times
> during simulation the whole box shrinks and then expands more than it
> did previous time; the change in proportion (elongation in z) is
> continuous.
>
> I ran simulations in NVT today just to see if it helps me keep the
> size of the box fixed and I still see the change in proportions and
> increase in Z, actually the whole box becomes much bigger, and
> proportions change as well, although not as much as it happens when I
> run NPT.
>
> Here is my configuration file for NVT:
>
> # Minimization and Equilibration of argon with PBC in XY
>
> structure ar.psf
> coordinates ar.pdb
> set outputname ar_force_out
>
> firsttimestep 0
>
> set temperature 310
>
> # 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
> rigidBonds none
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on
> langevinDamping 5
> langevinTemp $temperature
> langevinHydrogen off
>
>
> # 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 30
>
> # Constant Pressure Control (variable volume)
> useGroupPressure no ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.0
> langevinPistonDecay 50.0
> langevinPistonTemp $temperature
>
> tclForces on
> tclForcesScript my_force.tcl
>
> outputName $outputname
>
> restartfreq 500
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
>
> minimize 1000
> run 50000
>
> On Fri, Mar 11, 2016 at 3:34 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>> It is better to set cellbasisvector[1,2] to exact values.
>> Because you are not using MSM (and you can’t use PME with non-periodic systems), interactions between atoms in the system aren’t right (they are cut off at 12 AA). You should look into MSM first, it should not be that difficult.
>>
>> Now, the fact that your simulation crash ~150,000 steps might indicate a problem that emerges due to multiple time-stepping. Try: "stepspercycle 2".
>>
>> Finally, what do you expect to get from an NPT simulation with vacuum along z? How do you expect langevinPiston to work in this situation?
>>
>>
>>
>>> On Mar 10, 2016, at 20:01, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>>
>>> 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"?
>>>>>>
>>>>
>>
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