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Blocking pockets in MD?

Started by Kajum Safiullin, October 16, 2019, 04:42:04 PM

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Kajum Safiullin

Hi everyone,

I have to use blocking pockets in both MC and MD simulations. It works fine with MC, but doesn't work during MD simulations at all: gas molecules keep going inside the blocked pockets (they have open geometry in my case and are not surrounded by framework atoms). Any ideas how to solve this issue?

I will appreciate any help.


Hello Kajum,

It seems to me that block pockets only has an effect during Monte Carlo moves. So, in an MD simulation, when raspa is initially adding molecules to a framework to give the desired number, it will not allow their creation in blocked pockets. During MD however, if a molecule is able get into a pocket (a "side-pocket"), it will spend time there.

Why would want to block pockets in MD if the molecules are able to move into the pockets under normal circumstances given the structure, the force-field, and the conditions?

Blocking pockets is normally done on isolated pockets that don't communicate with accessible channels. If you want to block regions of a framework that are actually accessible during MD, then you have to decide where the boundary of the pocket is and your results will depend on the exact nature of what you block with. The blocking of isolated pockets during MC is somewhat different. If you fill the pocket with a hard-sphere, there will be a range of hard spheres that all give the same effect and do not modify anything happening outside the pockets.

Kajum Safiullin

Thank you for the information.
I am using raspa for a somewhat different than a gas in zeolite-like structures with closed pores, the system and its conditions are different to ones usually used in raspa simulations. However I found raspa as a nice code that suits my basic requirements for simple initial tests of a complicated system after some modifications of my structure with a side-pocket (as you called it). I'll think on new mods to solve my problem with MD.