VMD-L Mailing List

From: Rajan Vatassery (rajan_at_umn.edu)
Date: Sat Sep 15 2012 - 16:43:08 CDT

Erik and Marc,
        I would change one small thing in the command below originally sent by
Erik:

measure minmax [atomselect top all]

Instead of "all" I believe you would want to select a smaller subset of
your system. Presumably you have solvent molecules in your system, let's
say they have a segid "SLV" and your disaccharide has a segid of "SAC".
If you wanted to simply measure the minmax of segid SAC, you would use:

measure minmax [atomselect top "segid SAC"]

If you are unsure of the segid of your disaccharide, you can find a list
of segids in VMD under the Graphics --> Representations --> Selections
tab and then scroll to segid. The value field should have a list of
segids.

hth

rajan

On Sat, 2012-09-15 at 10:29 -0500, Martin, Erik W wrote:
> As a disclaimer, I'm not 100% certain what you're attempting to measure, but if all you want is the size of the molecule, you can use the "measure" function. My guess is that you'd want to use the "minmax" option that return the minimum and maximum xyz in your atomselection. The syntax would look something like this:
>
> measure minmax [atomselect top all]
>
> ... if this isn't what you're interested in, its likely that there is another measure function that will work
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node136.html
>
> You can, of course loop these over the whole trajectory if you're worried it will change.
>
> -Erik
> ________________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Marc Gordon [marcgrdn55_at_gmail.com]
> Sent: Saturday, September 15, 2012 7:15 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Determining the Size of my Molecule. .
>
> Hi all
>
> I recently got some rather good advice about my molecular dynamics simulations. Basically I'm now wanting to turn off the NAMD switching function and instead just truncate my electrostatic interactions at a particular distance in order ot reduce run times for my simulations.
>
> The thing is, I want to make sure that that cutoff distance I specify will include the entirety of my disaccharide of interest.
>
> My knowledge of VMD is rudimentary at best. I have used it a little in the past to check atom index numbers and to do a few simple atomselect commands but I haven't used it extensively. Does anyone have any advice on how to go about determining the size of my disaccharide? Would VMD be the tool to use for this sort of thing?
>
> I'm thinking the best approach would be to look at previous simulations and write a script that will run through it frame by frame finding the greatest distance between any 2 atoms in the disaccharide and print that value out to a file or even to the screen I suppose. That way once I find the greatest distance I can set the cutoff distance with a margin to allow for some movements I haven't yet seen in my past simulations. Would this be a good approach or are there other recommendations for better approaches?
>
>
> Thanks in advance everyone.
> Marc
>
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