Re: ABF simulations with singularities?

From: Junwoong Yoon (junwoony_at_andrew.cmu.edu)
Date: Mon Jul 09 2018 - 12:52:09 CDT

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
>> }
>>
>>
>>

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