Re: abf with colvars example

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Jun 04 2009 - 13:44:06 CDT

Hi David,

An updated tutorial is in the works. In the meantime, since there
seems to be high demand for it, here is a basic ABF example.
The NAMD config file would just contain the following extra lines:

colvars on
colvarsConfig distance-abf.in
# The next line is for restarting a previous run
#colvarsInput <some file name.colvars.state>

and the file distance-abf.in may read:
---------

colvarsTrajFrequency 10
colvarsRestartFrequency 10000

colvar {
  name d

  width 0.2
  lowerBoundary 5.0
  upperBoundary 15.0
  lowerWallConstant 10.0
  upperWallConstant 10.0

  distance {
    group1 {
      atomNumbers 1 2 3
    }
    group2 {
      atomNumbers 4 5 6
    }
  }
}

abf {
  colvars d
  fullSamples 500
}

-------------
Best,
Jerome

On Thu, Jun 4, 2009 at 1:53 PM, David A. Horita <dhorita_at_wfubmc.edu> wrote:
> Hi,
> I was trying to figure out how to split an ABF run into parts using the 2.6
> syntax but it looks like this is easiest in 2.7b1.  However, I'm a bit
> confused as to how to implement to colvar/abf component - do the abf
> commands go in the colvarsconfig file or the main input file, etc.  Is there
> an equivalent atom-based_01.conf (deca-alanine abf tutorial) for 2.7b1
> available?
>
> from the manual, I interpret xiMin-> lowerBoundary, xiMax->upperBoundary,
> dxi-> width, but I'm not sure how to assemble everything.
>
> Thanks,
> David
>
> -----------------------------
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine
> Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email:  dhorita_at_wfubmc.edu
> web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
>

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