Re: ABF calculation using RMSD

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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