Re: ABF-Zcoord:

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Feb 04 2009 - 18:13:50 CST

Yes, your approach seems reasonable (given the information you gave),
but as in all free energy calculations, and simulations in general,
certain results are not guaranteed. Specifically, only people who
know the specific system you're simulating can appreciate your choice
of reaction coordinate and the set of constraints you included.

If this approach fails, there may be other technical ways to do what
you're planning. For instance, you may want to have a look at the
collective variables module in the CVS version, that implements ABF on
a broader choice of reaction coordinates and can do multidimensional
sampling as well. If you see that zCoord is insufficient, you may add
x and y in the sampling rather than constraining them.

But basically, if a given reaction coordinate doesn't work, I'm afraid
you're mostly on your own to understand why.

Giacomo

---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
 phone: (+1)-215-573-4773
 fax: (+1)-215-573-6233
 mobile: (+1)-267-324-7676
 mail: giacomo.fiorin_<at>_gmail.com
 web: http://www.cmm.upenn.edu/
---- ----

2009/2/3 刘育 <supram_at_nankai.edu.cn>:
> Dear Namd developers,
> I am running a free energy calculation with ABF method for the
> complex of β-CD
> with L-glutamic acid (Glu) in waters. The abf coordinate is zCoord. When
> running the free energy calculation, the the abf abf1 { 14 35 56 77 98 119
> 140 }oxygens atoms of the β-CD are fixed; and I want to constraint the abf
> abf2 { 149 150 164 165 } oxygens atoms of the L-glutamic acid on the XY plan
> to make sure the L-glutamic acid (Glu)moving along the Z axis.
> Is my method reasonable? Is there other methods to make sure that the
> L-glutamic acid (Glu)moving along the Z axis?
> I will very be deeply grateful for your help, thank you very much!
> Here are my config file for the ABF simulation.
>
> structure bcdlglu_wb_na.psf
> coordinates restart.coor
> velocities restart.vel
> extendedsystem restart.xsc
> firsttimestep 1010000
>
> paraTypeCharmm on
> parameters par_all22_prot.inp
> parameters CSFF_parm.inp
>
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 14.0
> switching on
> switchdist 12.0
> pairlistdist 16.0
>
> timestep 1.0
> rigidbonds all
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
> langevin on
> langevinDamping 1
> langevinTemp 298.15
> langevinHydrogen on
>
> useGroupPressure yes
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1
> langevinPistonPeriod 100
> langevinPistonDecay 50
> langevinPistonTemp 298.15
>
> wrapwater on
> wrapall on
>
> PME on
> PMEGridSizeX 36
> PMEGridSizeY 36
> PMEGridSizeZ 60
>
> fixedatoms on
> fixedatomsfile bcdlglu_wb_na_f.pdb
> fixedatomscol B
>
> constraints on
> consref restart.coor
> conskfile bcdlglu_wb_na_h.pdb
> conskcol B
> selectconstraints on
> selectconstrx on
> selectconstry on
> selectconstrz off
>
> outputName output-ABF
> binaryoutput no
> outputEnergies 1000
> outputTiming 1000
> outputPressure 1000
> dcdfile bcdlglu_wb.dcd
> dcdfreq 1000
> dcdunitcell yes
> xstfreq 1000
> restartname restart-1
> binaryrestart no
> restartfreq 1000
>
> source /nfs/s09r2p2/yuliu_nk/NAMD2.6-1/Abf/abf.tcl
>
> abf coordinate zCoord
>
> abf abf1 { 14 35 56 77 98 119 140 }
>
> abf abf2 { 149 150 164 165 }
>
> abf ximin -8
>
> abf ximax -4
>
> abf dxi 0.1
>
> abf fullsamples 1000
>
> abf dsmooth 0.1
>
> abf forceconst 20
>
> abf applybias yes
>
> abf outputfreq 1000
>
> abf writexifreq 1000
>
> abf outfile bcdlglu.abf
>
> run 4000000
>

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