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Re: Check for the thermal stability of a 2D structure

dummy@example.com (fyzan) — Mon, 27 Jan 2020 14:39:43 +0000

Thanks it works, I was incorrectly pasting for 18 atoms while my structure has 12 atoms only

Re: Check for the thermal stability of a 2D structure

dummy@example.com (fyzan) — Mon, 27 Jan 2020 14:17:57 +0000

Sir after pasting above code in VMD console I get this error "ERROR
invalid atom id
invalid atom id"

Re: Check for the thermal stability of a 2D structure

dummy@example.com (sobereva) — Mon, 27 Jan 2020 14:02:50 +0000

Load the trajectory into VMD, and then copy below content to VMD console window to run, then you will find allbonds.txt in VMD folder, in which you can find length of each bond every 20 frames (each line corresponds to a frame).

set myfile [open allbonds.txt w]
set sel [atomselect top all]
for {set i 0} {$i<=2000} {incr i 20} {
puts $myfile "$i \
[measure bond {0 1 } frame $i] \
[measure bond {1 2 } frame $i] \
[measure bond {2 3 } frame $i] \
[measure bond {3 4 } frame $i] \
[measure bond {4 5 } frame $i] \
[measure bond {5 6 } frame $i] \
[measure bond {6 7 } frame $i] \
[measure bond {7 8 } frame $i] \
[measure bond {8 9 } frame $i] \
[measure bond {9 10} frame $i] \
[measure bond {10 11} frame $i] \
[measure bond {11 12} frame $i] \
[measure bond {12 13} frame $i] \
[measure bond {13 14} frame $i] \
[measure bond {14 15} frame $i] \
[measure bond {15 16} frame $i] \
[measure bond {16 17} frame $i] \
[measure bond {17 0} frame $i]"
}
close $myfile

Re: Check for the thermal stability of a 2D structure

dummy@example.com (fyzan) — Mon, 27 Jan 2020 11:22:39 +0000

sir I have successfully produced the RMSD curves. I'm fist time doing AIMD and learning from your paper. sir do you have any script for Fig. 26 Variation of all the eighteen C-C bonds in your paper? are the bondlengths are calculated manually after every 20 fs?

Re: Check for the thermal stability of a 2D structure

dummy@example.com (fyzan) — Sun, 26 Jan 2020 13:27:21 +0000

Thanks a lot Sir for the help.

Re: Check for the thermal stability of a 2D structure

dummy@example.com (sobereva) — Sun, 26 Jan 2020 13:18:23 +0000

fyzan wrote:

Dear Professor Tian LU,
sir can you please provide instruction for how to draw the figure of Root mean square deviation (RMSD) with respect to its optimized structure from AIMD simulations as shown in fig. 24 of your research paper "A thorough theoretical exploration of intriguing characteristics of cyclo[18]carbon: Geometry, bonding nature, aromaticity, weak interaction, reactivity, excited states, vibrations, molecular dynamics and various molecular properties"
Thanks in advance

It is very easy.
1 Boot up VMD program (http://www.ks.uiuc.edu/Research/vmd/)
2 Load the molecular dynamics trajectory to VMD
3 Select "Extensions" - "Analysis" - "RMSD Trajectory Tool"
4 Input "all" in the text box at upper right corner of the GUI, then click "ALIGN" button, select "Plot" check box, then press "RMSD" button. Then you will see the RMSD curve map.

If you need to plot multiple RMSD curves in the same map (as what I did in my paper), you need to make VMD export curve data for each trajectory to individual text file, then plot them together in e.g. Origin.

Re: Check for the thermal stability of a 2D structure

dummy@example.com (fyzan) — Sun, 26 Jan 2020 12:03:52 +0000

Dear Professor Tian LU,
sir can you please provide instruction for how to draw the figure of Root mean square deviation (RMSD) with respect to its optimized structure from AIMD simulations as shown in fig. 24 of your research paper "A thorough theoretical exploration of intriguing characteristics of cyclo[18]carbon: Geometry, bonding nature, aromaticity, weak interaction, reactivity, excited states, vibrations, molecular dynamics and various molecular properties"

Thanks in advance

Check for the thermal stability of a 2D structure

dummy@example.com (sobereva) — Wed, 30 Oct 2019 19:33:04 +0000

Today a people asked me a question on reasearchgate:

Thanks for you help the other time. Please, i want to check for the thermal stability of a 2D structure of about 55 atoms with gaussian09. i saw in one of your response that it can be done by ab inition molecular dynamics in gaussian09. Please, kindly help me on which keyword or method i need to apply in gaussian09.

Since my reply may be useful for other people, I paste my reply here:

I don't exactly know what the 2D structure you are studying. If it is a periodic system, you are unable to use Gaussian to perform AIMD for it, because despite that Gaussian supports periodic boundary condition (PBC) calculation, the speed is extremely slow, it is best to use first principle codes such as CP2K and Quantum Espresso to do the AIMD.
If your system is an isolated cluster, although Gaussian indeed can run AIMD for it, a better choice is using ORCA, because ORCA is freely available, faster, and meantime its AIMD function is easier to use.
It is doesn't matter even if you are not familiar with ORCA, because Multiwfn can easily create proper ORCA input file. Assume that you are using the latest version of Multiwfn, you can do this by inputting below commands in Multiwfn:
examples\CH3CONH2.fch // An example. You can also use .pdb/.xyz/.mol/.wfn...
100 // Other function
2 // Output file or create input file
12 // Create ORCA input file
AIMD.inp // The name of outputted file
0 // Select task
6 // Molecular dynamics
1 // Use B97-3c for the calculation. B97-3c is relatively cheap while reliable
Now you can find AIMD.inp in current folder. After properly changing it (the number of cores, memory, temperature and MD steps), you can run it by ORCA. The coordinate will be continuously dumped to pos.xyz in current folder during running. If during simulation, the system doesn't isomerize or dissociate, that means the system is stable under current simulation temperature.
If this calculation is too expensive for you, you can use xtb code developed by Grimme (https://github.com/grimme-lab/xtb/) to run molecular dynamics instead. The xtb is much faster, but the theory employed by xtb (i.e. GFN-xTB) is less reliable and accurate than B97-3c.