Re: About the err of "distanceZ"!

From: Jian Liu (bay__gulf618_at_sina.com)
Date: Mon Feb 22 2010 - 07:57:37 CST

> Dear all,
> 
> When I run the "hydration free methane" of "ABF tutorial", I found some wrong with this tutorial.
> 
> For ABF config file (Transport-widdown1.in):
> ...................................................
> distanceZ {
> group {
> atomNameResidueRange { OH2 1-955 }
> }
> group {
> atomnumbers { 1 2 3 4 5 }
> ..................................................
> 
> #> run "namd2 abf-window1.conf", then err happen:
> 
> "
> colvars:   Initializing a new collective variable.
> colvars:   # name = ProjectionZ
> colvars:   Initializing a new "distance projection on an axis" component.
> colvars:     # componentCoeff = 1 [default]
> colvars:     # componentExp = 1 [default]
> colvars:     Error: definition for atom group "main" not found.
> colvars:     If this error message is unclear, try recompile with -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
> "
> 
> It is obivous that it use the wrong syntax of "distanceZ". The distanceZ need add "main group" > and "ref group".
> 
> 1. But I do not know how to do it? who can help me write a config file of distanceZ or other 
> solve method?

The methods using "distanceZ/XY" component is much different with "distance" component. Please to reference
NAMD2.7 ug page93-94 for more information. I have read your input files ( thanks for your sending ), and will give the solvtion to your own problem. Please change the file "Transport-window1.in " with the following codes in place:

*   distanceZ {
*      main  {
*         atomnumbers { 1 2 3 4 5 }
*      }
*      ref {
*         atomNameResidueRange { OH2 46-48 }
*         psfSegID              WT1
*      }
*   }

The resid of each water molecules should be continuous, so you have to reprepare your pdb/psf files with psfgen. It is easy, isn't it.

> 2 And if I want to project a reaction coordinate on x- or y-axis, How do I 
> do? I do not find distanceX or distanceY?

You can changing the principal axis ('z' by default) by seting command "axis"
(ug page94) to a suitable value.

> 
> Thanks
> 
> javacfish

May I can help you.    

Jian Liu
Master-degree Graduate Candidate Majoring in Molecular 
Modelling
Outstanding Students and PhD. Wanted
CV: http://docs.google.com/View?id=ddgsqr48_1g4f3dmfq

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