Re: ABF simulations with singularities?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jul 09 2018 - 13:00:03 CDT

Hi Junwoong, as alternative to WHAM, since you are using distanceZ that
supports ABF, you can also run a metadynamics or umbrella sampling run with
the "writeTIPMF yes" option, which supported by other biases than ABF:

See examples here:
https://github.com/Colvars/examples/tree/master/tma-aco/smd-ti
https://github.com/Colvars/examples/tree/master/tma-aco/mtd-ti
https://github.com/Colvars/examples/tree/master/tma-aco/us-ti

This is a new feature, and you will need a nightly build of NAMD.

Giacomo

On Mon, Jul 9, 2018 at 1:53 PM Junwoong Yoon <junwoony_at_andrew.cmu.edu>
wrote:

> Hi Jerome,
>
> I tried this out, but still the molecule seems stuck in the lower or upper
> wall...
> Should I try harder wall or more overlap between grid boundaries and the
> harmonic walls?
>
> I also tried using Umbrella Sampling, but is there a way to reconstruct
> PMF profile without using WHAM?
>
> On Fri, Jul 6, 2018 at 3:18 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
>> Hi,
>>
>> I wonder if the variable could be getting stuck in the "gap" between the
>> boundaries of the force grid (beyond which there is no ABF bias) and the
>> wall potential - structly speaking there is no gap, but here the wall
>> potential is a little soft, so there is some space at the bottom of the
>> harmonic well. That is especially likely if the free energy is decreasing
>> towards the boundaries, which is an unusual situation because usually we
>> sample until the edges of a basin, but is still possible.
>>
>> What you could try is have the grid boundaries overlap with the harmonic
>> walls, and use a harder wall:
>> colvar {
>> name particleZ
>> width 0.1
>> lowerboundary 2
>> lowerWall 3
>> upperWall 30
>> upperboundary 31
>> lowerwallconstant 20
>> upperwallconstant 20
>>
>> Then the rest would be the same. You can restart this simulation from a
>> previous one to reuse the sampling you have. This will just extend the grid
>> by 1 Angstrom on either side.
>>
>> For the purpose of understanding precisely what's happening in your
>> existing simulations, you could try out this brand new visualization tool
>> for VMD:
>> https://github.com/Colvars/colvars/blob/master/vmd/scripts/cv_gui.tcl
>> Load a trajectory in VMD, then type "play <path/to>/cv_gui.cl" in the
>> console. Then you can load your Colvars configuration file, plot the
>> trajectory of selected variables, and navigate it by clicking in the plot
>> window.
>>
>> Best,
>> Jerome
>>
>>
>>
>>
>> On Fri, 6 Jul 2018 at 03:58, Junwoong Yoon <junwoony_at_andrew.cmu.edu>
>> wrote:
>>
>>> Hi all,
>>>
>>> I'm doing a simple adsorption energy calculations of a surfactant
>>> molecule onto a hard surface (graphene) in the presence of water molecules
>>> (water box) using ABF (with distanceZ colvar). Le'ts say the original
>>> z-direction coordinate of the surfactant as "z0", Then it only either goes
>>> down toward lowerBoundary or goes up toward upperBoundary. Then the
>>> simulation gets stuck near the boundary and does not explore the other way.
>>> It seems like without solvation box, it worked fine (simulation could
>>> explore the entire range in boundaries). However with the water solvation
>>> box, this thing happens.
>>>
>>> Here's what I have been tried but could not resolve this issue:
>>> 1) changing the grid limit (lower & upper boundaries)
>>> 2) changing original height, z0
>>> 3) increasing fullSamples value
>>>
>>> Please give me any recommendation if you ever seen this kind of issue
>>> before or have any idea to resolve it.
>>>
>>> FYI, I have copied my colvars and namd configuration files here.
>>>
>>>
>>>
>>> ######### CONFIG FILE ##########
>>>
>>> cellBasisVector1 51.05 0.0 0.0
>>> cellBasisVector2 0.0 51.579 0.0
>>> cellBasisVector3 0.0 0.0 70
>>> cellOrigin 0.0 0.0 0.0
>>>
>>> coordinates SDS_graphene_wb.pdb
>>> #extendedSystem SDS_graphene_wb.xst
>>> temperature 300
>>> XSTfile ./output/cntabf
>>> XSTfreq 1000
>>>
>>> set temp 300
>>> set numstep 10000000
>>>
>>> switching on
>>> switchdist 10
>>> cutoff 12
>>> pairlistdist 14.5
>>> margin 10.0
>>> stepspercycle 20
>>>
>>> #wrapWater on
>>> wrapAll on
>>>
>>> #useFlexibleCell no
>>> #useConstantArea no
>>> #useGroupPressure no
>>> langevinPiston on
>>> langevinPistonTarget 1.01325
>>> langevinPistonPeriod 200
>>> langevinPistonDecay 100
>>> langevinPistonTemp $temp
>>>
>>> langevin on
>>> langevinTemp $temp
>>> langevinDamping 0.5
>>>
>>> #This probably isn't necessary
>>> reassignFreq 100000
>>> reassignTemp $temp
>>>
>>> PME off
>>> PMEGridSizeX 108
>>> PMEGridSizeY 108
>>> PMEGridSizeZ 80
>>>
>>> #Use structures for molecule and a small number of graphene parameters
>>> structure SDS_graphene_wb.psf
>>> paraTypeCharmm on
>>> parameters par_all27_prot_lipid.inp
>>> parameters par_cntgraph.inp
>>> exclude scaled1-4
>>> 1-4scaling 1.0
>>>
>>> timestep 1.0
>>> #rigidBonds all
>>>
>>> fullElectFrequency 4
>>>
>>> numsteps $numstep
>>> outputtiming 1000
>>> outputenergies 1000
>>> outputname ./output/cntabf
>>> restartName ./restart/cntabf
>>> restartFreq 1000
>>>
>>> fixedAtoms on
>>> fixedAtomsFile SDS_graphene_wb.pdb
>>>
>>> DCDfile ./output/cnt_abf.dcd
>>> DCDfreq 1000
>>>
>>> colvars on
>>> colvarsConfig colvars_config_custom.tcl
>>>
>>> minimize 1000
>>> reinitvels $temp
>>> run $numstep
>>>
>>> ######### COLVARS FILE ################
>>> colvarsTrajFrequency 1000
>>> colvarsRestartFrequency 1000
>>> smp off
>>>
>>> colvar {
>>> name particleZ
>>> width 0.1
>>> lowerboundary 3
>>> upperboundary 30
>>> lowerwallconstant 5
>>> upperwallconstant 5
>>>
>>> distanceZ {
>>> #look this up in NAMD user guide
>>> main {
>>> atomsFile SDS_graphene_wb.pdb
>>> atomsCol B
>>> atomsColValue 1
>>> }
>>>
>>> ref {
>>> atomsFile SDS_graphene_wb.pdb
>>> atomsCol B
>>> atomsColValue 2
>>> }
>>> }
>>> }
>>>
>>>
>>> abf {
>>> name densityABF
>>> #timestepfactor 10
>>> colvars particleZ
>>> historyFreq 500
>>> outputFreq 1000
>>> fullSamples 500
>>> }
>>>
>>>
>>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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