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#2 Quantum Chemistry » How were temperature and pressure controlled in MD calculations? » 2023-04-21 15:23:48

Ahmed Wahba
Replies: 2

I made an MD in his manuscript and a comment came to me saying as follows
How were temperature and pressure controlled in MD calculations?

I have made the following comment:

In MD, physical properties are derived under isothermal, isobaric, or both conditions (NVT and NPT). When NVT is used, the thermostat adapts the kinetic energy of the particles to the target temperature by controlling their momenta. In the case of NVT, kinetic energy is determined by evaluating temperature, while in the case of NPT, it is determined by evaluating temperature and pressure. Dynamic simulations were traditionally conducted at a constant temperature as NVT, but production runs will continue to be conducted at constant energy (NVE).  There is a possibility that some thermostats will affect diffusion coefficients since they can interfere with system dynamics. The frame output interval was reduced and the number of steps increased to collect more data for analysis. So I only did 5,000 steps. Two charts are updated during the calculation. In one plot, power is plotted over time over different components, and in the other, the temperature is plotted over time. Since this is an NVE group arithmetic, the total power should be constant. The exchange of kinetic and potential energy should occur, but there should be no net exchange as long as the equilibrium lasts for a long time. It should also fluctuate around 300 K on average without a systematic change, and the pressure should average 1 atm or 0.0001GPa to obtain a balanced system.

His response to me was as follows:

Their reply to my nineth comment is wrong. However, they did not apply even this wrong reply in the revised manuscript. temperature can be controlled by applying thermostat or heat bath and velocity rescaling whereas the pressure is fixed by applying barostate or volume rescaling.
C9. How were temperature and pressure controlled in MD calculations?

Please, Doctor, can you explain to me the answer to this comment?

#3 Re: Quantum Chemistry » IR for metal organic framework » 2023-04-03 01:11:26

Thank you very much, dear Professor Beijing
But I have a problem if you can help me solve it.
Where I downloaded the program from the home page, but I can not install it.
Where the image below appears, and I cannot complete the installation process.
Untitled.png

#4 Quantum Chemistry » IR for metal organic framework » 2023-04-01 23:05:13

Ahmed Wahba
Replies: 3

please, how can i do the IR for metal organic framework in  Gaussian 09?

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