From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Mon Mar 14 2016 - 11:24:35 CDT
Hi Olya,
Yes, I meant langevinPiston. lagevin is for temperature control. You have to use langevin because you are using some mysterious tclForces that might heat up your system.
Maxim
> On Mar 11, 2016, at 21:42, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>
> Maxim,
>
> thanks!
>
> Do you mean "langevin on" or "LangevinPiston on"? I thought "langevin
> on" controls temperature. If not, I am confused. I saw a couple of
> sample configuration files marked as NVT simulation where langevin is
> set to on... Are you saying that for NVT I need to comment it out as
> well?
>
> If you meant LangevinPiston, I just commented it out and ran another
> job and my simulation doesn't do anything crazy now. I also used exact
> measurements for cellbasis vectors.
>
> Olga
>
> On Fri, Mar 11, 2016 at 4:31 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>> 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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