[gmx-users] NVT ensemble for simulating of carbon nanotube (as drug delivery)

[Justin Lemkul]

On 7/8/19 3:22 AM, afsaneh maleki wrote:
> Hi all
> I have two questions:
>
> 1-      Is it correct to apply statistical ensemble NVT (N=constant,
> T=constant) for simulating of carbon nanotube (as drug delivery)?  It
> doesn’t leads to a pressure in the system that is far from normal pressure?
> Some Author use VNT and the other use NPT. In the other word, when we can
> use NVT ensemble to simulation CNT (as drug delivery)?

The ensemble should be chosen based on which conditions are relevant to 
the simulation. Perhaps some people use NVT simply to side-step any 
possibility of compression along the CNT axis; sometimes models are 
simplified in this way. Perhaps that's not the most accurate. That's 
your job to decide what is the best model for the questions you are 
trying to answer.

> 2-      How to distinguish between infinite CNT and finite CNT with command
> in .mdp file?

The main difference is in the topology, but in the case of an infinite 
CNT, you must use "periodic_molecules = yes" in the .mdp file. Proper 
bonds must be specified in the topology.

-Justin

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Justin A. Lemkul, Ph.D.
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