From: Marc Gordon (marcgrdn55_at_gmail.com)
Date: Sun Sep 16 2012 - 05:21:29 CDT

Actually determining the minimum and maximum xyz of my molecule sounds
perfect. That is the sort of thing I am looking for. I am glad there is
already a function present that can do that for me. Makes it much easier.

Basically I want to know how far I need to allow the electrostatic
interactions to extend in the system before they are cut off. Getting the
maximum of the xyz should give me the value I can use as a cutoff to ensure
that the electrostatic interactions influence the whole molecule and don't
get cut off too early.

I will look into looping through a trajectory. I imagine one could utilise
the 'for' construct? I am already relatively familiar with the syntax of
'for' in Tcl but I am not familiar with how one would go about looping
through the whole trajectory. I imagine it shouldn't be difficult to find
in a guide but if you wish to point me in the right direction I wouldn't
say no. :)

Thank you for the help so far this is great. The capabilities of VMD never
cease to amaze me.
Marc

On Sat, Sep 15, 2012 at 5:29 PM, Martin, Erik W <Erik.Martin_at_stjude.org>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
>
> Email Disclaimer: www.stjude.org/emaildisclaimer
> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
>
>