From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Thu Feb 24 2011 - 12:42:02 CST

Hello Peter,
Thank you for your reply. Here are more details of my calculations.

First, I load in 1 pdb file 1 dcd file with stride 10. So I have 201 total structures. For testing purposed I just wanted to take a small sample of that 200, say every 10 structures for a total of 20. It would appear that stride in the gui would do this for me. However, if I understand what you are saying, is that this switch is only to correlate the labeled timestep with whatever the original timestep was for the dcd file I read it. That is, since I already did used a "real" stride of 10 when reading the dcd file into vmd then I should set stride in the gui for 10 to keep timesteps on track. Is that the correct understanding? The namdgui stride switch does not do a further downselect of frames? Skip just blows through X frames and then starts up at the regular granularity of 1.

Unfortunately I cannot send a structure at the moment to help address the second selection problems.
But as I stated in the first email. The only selections that I have been able to get to work are single residue pairs. For instance if the first selection field contains: resid 203 and protein and the second selection field contains: resid 124 and protein. I get the appropriate plots and data files showing the forces and energies. However, if the second selection contains: protein and same residue as within 6 of resid 203 and protein then the calculations "proceeds" but at the end, the plot and data file contain only zeroes.

Can you send me your example and I can test it?

Brian

-----Original Message-----
From: Peter Freddolino [mailto:petefred_at_ks.uiuc.edu]
Sent: Wednesday, February 23, 2011 5:30 PM
To: Bennion, Brian
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: vmd1.9beta1

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
>
>
>
>
>
>
> Biosciences and Biotechnology Division
> Lawrence Livermore National Laboratory
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