From: Hugh Martin (hughtendo_at_gmail.com)
Date: Thu Aug 27 2009 - 23:41:18 CDT
Yikes, those are indeed quite different! I was previously unaware of the
different indices.
Thanks indeed for the help.
Hugh
2009/8/27 Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
> Hugh,
> Just making sure of one thing - you are providing ABF with 1-based
> atom indices, as in PDB files, not the 0-based indices from VMD? In
> VMD, the 1-based index is called "serial".
>
> Eric: thanks for replying. I think Hugh is using zCoord from the NAMD
> 2.6 implementation, not the more flexible distanceZ from the colvars
> module...
>
> Best,
> Jerome
>
> On Thu, Aug 27, 2009 at 11:30 AM, Hugh Martin<hughtendo_at_gmail.com> wrote:
> > Hello,
> >
> > I wonder if anyone else has experienced this issue: the Xi parameter for
> a
> > zCoord-1atom reaction coordinate (the Cartesian z-axis distance between
> atom
> > abf1 and abf2) is outputting incorrect values in my simulations. For
> > instance in one of my simulations, abf1 and abf2 are chosen as two oxygen
> > atoms, each belonging to a separate water molecule, these are precisely
> > 4.4345 Angstroms apart in the z-direction at the start of my simulation,
> > however, in the log file the Xi output reads "TCL: ABF> Xi at timestep 0
> :
> > 104.585426303", this large value of Xi is not the result of a measurement
> > through the periodic image, as the waterbox is over 130 Angstroms in
> height,
> > making 104.6 Angstroms impossible in either direction.
> >
> > This is a 330k atom system and seems to produce very random values for Xi
> > depending on the pair of atoms I choose for abf1 and abf2, sometimes
> being a
> > negative or positive value independent of whether abf1 or abf2 is higher
> in
> > the z-direction. This occurs in both NAMD2.6 and NAMD2.71b.
> >
> > Any help on the matter will be greatly appreciated.
> >
> > Many thanks,
> >
> > Hugh
> >
> >
>
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