VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Mar 15 2018 - 08:39:14 CDT

Try adjusting the contour level in the representation to see where the
highest density is.

Giacomo

P.S. Spam filters can recognize any "remove" or "at" tricks to protect
email addresses, and using them would only slow down the humans.

On Thu, Mar 15, 2018 at 8:16 AM, Saikat Pal <saikatpaliitg_at_remove_yahoo.com>
wrote:

> Dear VMD users,
> Recently I have used Volmap Plugin to calculate spatial distribution
> function or probable density. I have used the following command:
> selection: resid 16 to 22 and within 5.0 of resid 3 4
> molecule: abc.prmtop (generated from amber trajectory)
> volmaptype : density
> resolution: 1.0
> atom size: 1.0
> weights: mass
> tick on the: compute for all frame avg
>
> I have got this kind of image (I have attached the test.png). My question is
> : Are the all command is correct ?
> And Why the density is cubic in my case ??
>
> Thanks
> Saikat
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin