VMD-L Mailing List

From: Marc Gordon (marcgrdn55_at_gmail.com)
Date: Sat Sep 15 2012 - 07:15:28 CDT

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