VMD-L Mailing List

From: Gabby Leonard (gabbyleonard94_at_gmail.com)
Date: Thu May 11 2023 - 16:27:33 CDT

Thanks, Josh.
What a relief - I thought there was something seriously wrong with my
simulations!

On Thu, May 11, 2023 at 3:13 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> Hi Gabby,
>
>
>
> The way trajectory smoothing works in VMD is to visualize the average
> position for an individual atom across multiple frames. This has the
> desired smoothing effect to make individual motions less jittery, but it
> also has the undesired effect of making things that move quickly (like
> rotating methyl groups) look ridiculous, since the average position is not
> guaranteed to be in a physically reasonable place. If I am doing analysis,
> I typically will not use smoothed coordinates, since it edits the
> coordinates. However, if I’m trying to make a movie that looks good and
> makes a point, I may use trajectory smoothing and hide hydrogens/aromatic
> rings (which wink! Its very silly) in visualization.
>
>
>
> -Josh
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Gabby Leonard <
> gabbyleonard94_at_gmail.com>
> *Date: *Thursday, May 11, 2023 at 5:04 PM
> *To: *"vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: Trajectory Smoothing and length of hydrogen bonds
>
>
>
> Hello,
>
>
>
> I ran a simulation with NAMD and have the rigid bonds parameter activated
> for all bonds involving hydrogens. When I play my simulation at normal
> speed in VMD there is no problem, however when I apply trajectory smoothing
> (window 5), the length of the hydrogen bonds is variable and the side chain
> H-bonds don't look normal. I have attached two images to better describe my
> problem. Any suggestions on why this may be occurring and how to fix it? I
> unwrap most of my simulations, but have tried this with wrapped simulations
> and the same phenomenon occurs.
>
>
> Thanks,
>
> Gabby
>