From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Tue Mar 15 2016 - 14:48:58 CDT
Maxim,
thank you for replying to my questions. To conclude this thread I
wanted to add, that after running a huge number of jobs in both (what
I think is) NVT and NPT I noticed that --
1) When I run NVT with CellBasis3 commented out my box elongates in Z
direction, so commenting it out is not equivalent to setting up a hard
wall. I think if I run it very long it will just keep stretching to
infinity or the limit that's allowed in namd. The size in X and Y
holds well.
2) I don't have a margin problem when I do NVT, it only happens when I
run NPT and only when I comment out CellBasis3. I think that is
because there is nothing in Z direction, so unless I use different
method for setting up a wall there, the data will make no sense.
I am trying to figure out MSM now, but that would be a subject of
another thread.
Olga
On Mon, Mar 14, 2016 at 12:24 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> 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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