From: Bennion, Brian (
Date: Fri Feb 25 2011 - 10:45:04 CST

Thank you Peter for the reply.
Yes I was confused on the skip switch and it does in fact work as stated.

The atomselection is still a bit puzzling, just want to confirm what you said. There are some instances in vmd when a group of atoms is selected based on a distance to some other reference object(s), the reference object is not included. From your description below, it sounds like the selections I make in the plugin are including the reference object(s) in its selection because the resname SSON is also part of the protein. Is that correct?

Thank you for the fixes.


-----Original Message-----
From: Peter Freddolino []
Sent: Thursday, February 24, 2011 7:04 PM
To: Bennion, Brian
Subject: Re: vmd-l: vmd1.9beta1 namdEnergyPlugin

Hi Brian,

Regarding switch/skip, your understanding of stride is correct in terms
of how it is documented and intended, but the timestep and stride
functionalities appear to be broken for some reason. I have just patched
them, so they should now work in the cvs version. However, in my tests
skip **is** working as documented -- skip n causes calculation only for
every nth frame, it does not simply skip n frames at the beginning.
Could you confirm that you see unexpected behavior here?

Regarding the selections, I think the problem here is that the atoms in
selection 1 are also part of selection 2. Because pairinteractions in
namd require interacting atoms to be flagged with a 1 or a 2 in the
occupancy or beta field to correspond to group 1 or group 2, you end up
with zero atoms in group 1 because those atoms are also in group 2. This
also explains why things work ok when you switch the order of the
selections. In the fix I just committed there is now a check for this
situation, which should give an informative error when it occurs.

Please let me know if this fixes things.

On 02/24/2011 01:42 PM, Bennion, Brian wrote:
> 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 []
> Sent: Wednesday, February 23, 2011 5:30 PM
> To: Bennion, Brian
> Cc:
> 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
>> 7000 East Ave Livermore California 94550
>> phone:925-422-5722
>> fax:925-424-4334