Re: Free energy of conformational change

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri May 29 2009 - 11:31:00 CDT

Hi Branko,

The following parameters:
fullSamples 200
hideJacobian no
outputFreq 5000
applyBias yes

are ABF-specific; they should be in the abf block.

Also, the line dumpFreeEnergyFile yes is not needed. ABF will always
write the PMF to disk in 1d calculations.

Best,
Jerome

On Fri, May 29, 2009 at 7:44 AM, Branko <bdrakuli_at_chem.bg.ac.yu> wrote:
> Chris, Giacomo,
>
> Likely that I can setup ABF configuration for 2.7b1. It is sufficient to add
> two lines in NAMD configuration:
>
> colvars    on
> colvarsConfig    triiPrcol
>
> But there is two problems minor and major:
>
> According to namd out, next lines from colvar (and ABF) configuration are
> not recognized:
>
> fullSamples    200
> hideJacobian    no
> outputFreq    5000
> applyBias    yes
>
> But this not influence on calculation. The second fatal on calculation is
> that first atom in the first group of atoms can nor be recognized, I am
> trying with different definition of those atoms as 1 3 5 or 1-6 (implied
> centroid on the one phenyl ring) with same results. Atom numbering are taken
> from input PDB file.
> To be clearer, below are colvar configuartion, and below the line part of
> namd out file. Please advise me to overcome the problem.
> Thanks
>
> Branko
>
> colvar/abf configuration:
>
> colvarsTrajFrequency    1
> analysis    on
> fullSamples    200
> hideJacobian    no
> outputFreq    5000
> applyBias    yes
>
> colvar {
>
>    name d
>
>    lowerBoundary  3.88
>    upperBoundary 9.60
>    width 0.2
>
>    distance {
>        group1 { 1 - 6 }
>        group2 { 16 17 18 }
>    }
> }
>
> abf {
>    colvars d
>    dumpFreeEnergyFile yes
> }
>
> ___________________________________-
>
> colvars:
> ----------------------------------------------------------------------
> colvars: Initializing the collective variables module, version 29-09-2008.
> colvars: # colvarsTrajFrequency = 1
> colvars: # colvarsRestartFrequency = 1000 [default]
> colvars: # trajAppend = off [default]
> colvars: The restart output state file will be
> "C:\Namd\246triiPrinterASAheatdyn.restart.colvars.state".
> colvars: The trajectory file will be
> "C:\Namd\246triiPrinterASAheatdyn.colvars.traj".
> colvars: The final output state file will be
> "C:\Namd\246triiPrinterASAheatdyn.colvars.state".
> colvars: # analysis = on
> colvars:
> ----------------------------------------------------------------------
> colvars: # readTrajectory = "" [default]
> colvars: # readBegin = 0 [default]
> colvars: # readEnd = 0 [default]
> colvars:
> ----------------------------------------------------------------------
> colvars:   Initializing a new collective variable.
> colvars:   # name = d
> colvars:   Initializing a new "distance" component.
> colvars:     # componentCoeff = 1 [default]
> colvars:     # componentExp = 1 [default]
> colvars:     # oneSiteSystemForce = off [default]
> colvars:       Initializing atom group "group1".
> colvars:       Error: keyword "1" is not supported, or not recognized in
> this context.
> colvars:       If this error message is unclear, try recompile with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
>
>
>
>
>
> Chris Harrison wrote:
>
> Branko,
>
> I'm responding to your earlier email, which I marked for follow up, but
> didn't do before Giacomo replied with a very reasonable answer.  Do you need
> further help with an example ABF or metadynamics input file or was your
> question resolved?
>
>
> Chris
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu                            Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
>
>
>
> On Wed, May 20, 2009 at 6:15 AM, Branko <bdrakuli_at_chem.bg.ac.yu> wrote:
>>
>> Hallo Chris,
>>
>> I am note the respond to Lixia, so I need something similar - to obtain
>> (only) the free energy of conformational change on small (flexible)
>> molecules in two explicit solvents. Using ABF on ver. 2.6 and defining
>> distance between two groups of atoms in studied molecule works without
>> problem, but using colvar on 2.7b1 (which offer plenty of possibility) looks
>> something more complicated. So, please if some example of configuration file
>> is available, let me know.  2.7b1 ug give more than sufficient information,
>> but I have no experiences with making of input (configuration) for such
>> calculations. Likely that all atoms in molecule can be used for free energy
>> of conformational change evaluation.
>> Thanks in advance
>>
>> Branko
>>
>>
>
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