VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Sep 16 2012 - 17:10:21 CDT

On Sun, Sep 16, 2012 at 12:21 PM, Marc Gordon <marcgrdn55_at_gmail.com> wrote:
> 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. :)

there are scripting examples for analysis in the
VMD user's guide. and more in the VMD tutorials.

axel.

>
>
> 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
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.