From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Feb 15 2011 - 04:46:25 CST
Hi Maiti,
This looks mostly like a side effect of enabling hideJacobian for a
coordinate for which it is not appropriate (for small values of RMSD,
the Jacobian contribution is huge). The default is off - don't change
it.
Cheers,
Jerome
On 15 February 2011 02:08, Buddhadev Maiti <chebm_at_langate.gsu.edu> wrote:
> Dear NAMD Users,
> I am performing ABF calculation using RMSD as a collective variable. I am using NAMD-2.7 version. My Distance.in file is in below. But in prod1.colvars.traj file I am getting RMSD values which are not in between 0.742 and 2.742. The prod1.colvars.traj is big file, so I am sending some of the values. Could anybody can suggest me any problem in Distance.in file, it will be great help for me.
> Have a nice day,
> Thanks,
> Maiti
>
> Distance.in
> Colvarstrajfrequency 1000
> Colvarsrestartfrequency 1000
> colvar {
> name GRrmsd
> width 0.1
> lowerboundary 0.742
> upperboundary 2.742
> lowerwallconstant 100.0
> upperwallconstant 100.0
> rmsd {
> atoms {
> atomsFile 10.pdb
> atomsCol O
> atomsColValue 1.0
> }
> refPositionsFile ep.pdb
> refPositionsCol O
> refPositionsColValue 1.0
> }
> }
> abf {
> colvars GRrmsd
> fullSamples 1000
> hideJacobian
> }
>
> prod1.colvars.traj:
> 20000 8.80246428132221e-02
> 21000 8.80608759027566e-02
> 22000 8.46306414199712e-02
> 23000 9.66174831058771e-02
> 24000 9.94028080033878e-02
> 25000 8.68121250316395e-02
> 26000 8.61812497752078e-02
> 27000 9.75722872880951e-02
> 28000 9.28331687685522e-02
> 29000 8.47315102606470e-02
> 30000 9.97560581467597e-02
> 31000 1.00552660409621e-01
> 32000 8.92195009776420e-02
> 33000 8.92411507759293e-02
>
>
>
>
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