Using SageMD for molecular dynamics

[cbaykam]

Hi ;
Is there anybody using SageMD for molecular experiments. I am planning to set up a mail group for SageMD or all the molecular dynamics simulator software. Please write me if you want to join or if you know any other place for me to find anyone please tell me... Thank you all...

 

[marlon]

Hi ;
Is there anybody using SageMD for molecular experiments. I am planning to set up a mail group for SageMD or all the molecular dynamics simulator software. Please write me if you want to join or if you know any other place for me to find anyone please tell me... Thank you all...

Just want to let you know if you are really sure that molecular dynamics (MD) are really necessary for your goals. I mean, this software requires tremendous amount of computational effort and time. Do you have the necessary resources (parallel supercomputers and all). Keep in mind that in most of the case MD is not even necessary because you can bypass it by being smart.

Let me give you this example : suppose you want to know the temperature dependence of a semiconductor/metal interface. The best way to model that is MD. But there is a way out : suppose the interface is studied at 900 degrees C and 400 degrees C. Then measure (with AFM for example or TEM) the crystalline structure of the SC and the metal. At each temperature value, this structure will be different. Then, you use this crystalline structure as the imput for the simulations. This will go much much faster and you will find out how the interface electrostatics will change with temperature. At least you will have a qualititive insight in what is going on.

You see ?

marlon