VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Apr 19 2018 - 17:48:05 CDT

Would saving more frequently help with waters jumping too far? Is the command just pbc unwrap or do I do something like pbc unwrap water or pbc unwrap resname TIP3?

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Thursday, April 19, 2018 4:39:37 PM
To: vmd-l_at_ks.uiuc.edu; McGuire, Kelly
Subject: RE: Smoothing

Hi Kelly,

What smoothing does is really simple: it calculates the average position of each atom over the number of frames you tell it to, and displays that instead of the "true" position. For molecules that don't move very much between frames, this takes out the high-frequency motions and results in a trajectory that is less likely to induce seizures when played back quickly. Water (and other small molecules) move a TON between frames. If you have wrapAll or wrapWater turned on during simulation, it is likely that a water molecule will jump from one side of the periodic cell to another. Since smoothing is just an average position, that jump means that a water molecule might move significantly between frames. Using pbc unwrap will usually fix this (at the cost of making your water "box" become less box-like over time), however, depending on the simulation time between dcd frames, water may actually move several box lengths, making unwrap unreliable.

-Josh

On 2018-04-19 16:06:51-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

Question about smoothing a trajectory. I did the explicit water ubiquitin NAMD tutorial under QwikMD tutorials. I am trying to learn about smoothing a trajectory. I load the simulation psf file and then the dcd into VMD. When I play the dcd without smoothing, the waterbox fluctuates normally, but really fast due to the thermal noise. I tried smoothing the trajectory for the water in the representations -> trajectory, but the water box does something strange when smoothing is applied. I tried including two pics, one where the waterbox looks normal during the trajectory, and the second with smoothing, but looks like I couldn't send them. What does smoothing do to the waterbox? I just wanted to see the waters moving more smoothly and slowly instead of jumping around because of thermal fluctuations. I did read something about unwrapping the trajectory, but that didn't really seem to help...unless I did it incorrectly.

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602