From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Thu Jun 04 2009 - 15:17:42 CDT
Thanks a lot Jerome,
This is answer on my question on atom group definition for abf in 2.7,
my simulation now works. Obviously problem is in syntax.
Branko
Jerome Henin wrote:
> 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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