Re: Regarding ABF Simulation

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Mon Sep 14 2009 - 15:34:17 CDT

Jagan, if you ruining ABF in NAMD 2.7b1, you should make separate file
for ABF input (see below) and add only

Colvars on
colvarsConfig name of colvar config. file (syntax given below)

Likely that you run ABF at 2.6, so try to change

"set ABFdir ./abf-1.8
source ./abf-1.8/abf.tcl"

with

"source ./abf-1.8/abf.tcl
package require abf"

And check do you have really /abf-1.8/abf.tcl where you define in input.

Hope this help.

Colvar definition for distance between two group of atoms:

colvarsTrajFrequency 1
colvarsRestartFrequency 10000
analysis on

colvar {

   name d

   lowerBoundary number - minimal expected in Angstroms
   upperBoundary number -maximal expected in Angstroms
   width 0.01

   distance {
       group1 {
          atomnumbers atom niumber(s)
       }
       group2 {
          atomnumbers atom number(s)
       }
   }
}

abf {
   colvars d
   fullSamples 500
   hideJacobian no
   outputFreq 1000
   applyBias yes
}

_________________

Jagan Mohan wrote:
> Hello Everyone,
> I am running an ABF Simulation with the distance parameter. When I
> start the job on 4 processors i get the following error.
>
>
> FATAL ERROR: Setting parameter TclForces from script failed!
>
>
> This are the lines in my input file
>
> # ABF SECTION
> set ABFdir ./abf-1.8
> source ./abf-1.8/abf.tcl
> # ORDER PARAMETER
> abf coordinate distance
> abf abf1 8846
> abf abf2 9876
> abf xiMin 5.0
> abf xiMax 34.0
> abf dxi 0.1
> # SAMPLING
> abf fullSamples 500
> abf dSmooth 0.1
> abf forceConst 10.0
> abf writeXiFreq 100
> # OUTPUT
> abf outFile full_run.abf
>
>
> Could anyone tell me what is wrong.
>
>
> Thanks and Regards,
> Jagan Mohan
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