Re: ABF simulation

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Sat Jan 07 2012 - 05:16:24 CST

Hi,

>From the files you attached, I can't see what the problem is, because I
don't know the z coordinate of the reference atoms (alpha carbons).

The first thing to check is the colvars.traj file, to see if the values
there match what you expect from inspecting the trajectory.

Best,
Jerome

On 6 January 2012 17:53, Tugba Nogay <gntuba_at_yahoo.com> wrote:

> Hello,
>
> I am trying to set up ABF simulations to get PMF of ion translocation
> through a membrane channel. My inputs are copied below. I noticed (through
> visual inspection, also wrote out pdb files for atom index 96913) that the
> ion that the forces are applied to moves out of the range even though I
> specify 100 kcal/mol-A force constant to upper and lower wall (I also tried
> 1000). There may be an apparent mistake that I can't see. I would
> appreciate it if someone can point out where the problem is.
>
> Configuration file:
>
> margin 2.5
> # protocol params
> firsttimestep 0
>
> # initial config
> coordinates window5.pdb
> temperature 323.15
> #velocities efw12.vel
> seed 13579
> #extendedSystem mid1.xsc
>
> # output params
> outputname mid1
> binaryoutput no
> restartname mid1
> restartfreq 10000
> DCDfile mid1
> DCDfreq 2000
> DCDUnitcell yes
> outputEnergies 2000
> outputPressure 2000
>
> colvars on
> colvarsConfig mrestrain2.in
>
> #outputSystemForce 1000
> #outputAppliedForce 1000
>
> # integrator params
> timestep 0.5;
> nonbondedFreq 1;
> fullElectFrequency 1;
>
> # force field params
> structure ../step5_assembly.xplor.psf
> paraTypeCharmm on
> parameters ../toppar/namd/par_all22_prot.prm;
> parameters ../toppar/namd/par_all27_na.prm;
> parameters ../toppar/namd/par_allxx_sugar.inp;
> parameters ../toppar/namd/par_all36_lipid.prm;
> parameters ../toppar/namd/par_all36_cgenff.prm;
> parameters ../toppar/namd/toppar_water_ions.str;
>
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 10.0
> cutoff 14.0
> pairlistdist 16.0
> stepspercycle 20
>
> # periodic boundary conditions
> cellBasisVector1 108.879 0.0 0.0
> cellBasisVector2 54.4395 94.0703 0.0
> cellBasisVector3 0.0 0.0 97.992
> cellOrigin 0.0 0.0 1.0395;
> XSTfile middlex
> XSTfreq 2000
> wrapWater on
> wrapAll on
> wrapNearest on
>
> # PME
> PME on
> #PMEGridSpacing 1.0
> PMEInterpOrder 6;
> PMEGridSizeX 148
> PMEGridSizeY 148
> PMEGridSizeZ 96
>
> # Dynamics
> rigidBonds water
>
> useGroupPressure yes;
> useFlexibleCell yes;
> useConstantRatio yes;
>
> langevin on;
> langevinPiston on;
> langevinPistonTarget 1.01325;
> langevinPistonPeriod 100.0;
> langevinPistonDecay 50.0;
>
> langevinPistonTemp 323.15;
> langevinTemp 323.15
> langevinDamping 1
> langevinHydrogen off
>
> # Execution script
> run 100000
>
> Colvars input:
>
> colvarsTrajFrequency 1000
> colvarsRestartFrequency 1000
> colvar {
> name Translocation
> width 0.1
> lowerboundary -6.00
> upperboundary 0.0
> lowerwallconstant 100.0
> upperwallconstant 100.0
> distanceZ {
> main {
> atomnumbers { 96914 }
> }
> ref {
> atomnumbers {
> 5 822 1579 2391 3165 3942 4737 5513 6297
> 7082 7857 8631 9441 10225
> 29 841 1603 2410 3177 3953 4756 5524 6308
> 7097 7873 8651 9452 10239 ...... ---> CA atoms of the protein
> }
>
> }
> axis ( 0.0, 0.0, 1.0 )
> }
> }
> abf {
> colvars Translocation
> fullSamples 1000
> }
>
> From window5.pdb:
> ATOM 96912 SOD SOD S 10 -51.392 30.755 -44.335 0.00 0.00
> SOD
> ATOM 96913 SOD SOD S 11 -19.337 27.654 42.819 0.00 0.00
> SOD
> ATOM 96914 SOD SOD S 12 7.290 7.262 -5.057 1.00 0.00
> SOD
> ATOM 96915 SOD SOD S 13 -11.144 5.802 -31.093 0.00 0.00
> SOD
> ATOM 96916 SOD SOD S 14 8.680 16.387 42.718 0.00 0.00
> SOD
>
> Thanks,
> TNogay
>
>
>
>

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