VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Feb 23 2011 - 19:30:06 CST

Hi Brian,
I think there may be some confusion about the usage of stride, skip, and
step length. Stride and step length are purely for bookkeeping purposes,
and help make sure that the times listed in the output match up with
your real timestep. What you're after is probably the skip argument.

Regarding selections, that sort of thing should work just fine, and
indeed, does when I try it on typical test systems. Could you give an
exact example of input structure and arguments where it fails?

Thanks,
Peter

On 02/23/2011 03:21 PM, Bennion, Brian wrote:
> It would appear that there is a small problem with the namdenergy plugin. The gui allows for a stride entry to be made, however, it appears to be ignored when you receive the eventual energy/force plot. For example, I have 201 frames loaded in vmd and with a stride setting of 100 I still have 200 data points in the plot. This behavior is the same in vmd1.8.7.
>
> In addition, it would also seem that a "protein and same residue as within 6 of resname blah" in the second selection is not supported. Only values of zero are reported in the final plot and data file. Is the plugin supposed to be able to accept this type of atom selection query?
>
> Thanks
> Brian Bennion
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>
> Biosciences and Biotechnology Division
> Lawrence Livermore National Laboratory
> 7000 East Ave Livermore California 94550
> phone:925-422-5722
> fax:925-424-4334
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>