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#1 2020-05-14 21:53:10

Registered: 2020-05-14
Posts: 1

vdW-potential: superposition of MD-results

Dear Dr. Lu,

First of all, thank you for your efforts in the development and constant improvement of MultiWFN-software.

In your recent preprint (Van der Waals potential: an important complement to molecular electrostatic potential in studying intermolecular interactions) you have successfully demonstrated the importance of analysis of van der Waals surface.

Particularly, the superposition of Ne atoms for all MD frames (Fig. 10) looks quite attractive for the action spectroscopy field, where neutral gas molecules driven mostly dispersion interactions are weakly bound to gas-phase ions. I am wondering how can one visualize it using MultiWFN+VMD software?

Looking forward to hearing from you.


#2 2020-05-15 08:33:38

Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 684

Re: vdW-potential: superposition of MD-results

Thank you for your attention to my new work. Here I describe how to generate figure 3 and similar effect of figure 10 of my paper:

(1) Load trajectory file, then use align tool in VMD (extensions - analysis - RMSD trajectory tool) to align the host molecule to eliminate its overall motion
Note that in VMD, each unconnected fragment has a unique fragment index. In current case, helicene is fragment 0.

(2) Enter Graphics - Representation, set plotting setting as follows. In the "trajectory" tab, let VMD simulatneously show all frames

(3) Set plotting and coloring style as follows, you can obtain figure 1 in my vdW potential paper

(4) If you prefer style of figure 10 of my paper, changing material and color as follows
Note that in order to avoid the superposition map is too dense, in the "trajectory" tab, I changed 0:50000 to 0:10:50000, namely the particle is drawn every 10 frames.


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