Reg: Forming a group of specific atoms in an user defined region.

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1

Dear All,

I am trying to study the interaction between water and CNT through MD and have a simulation domain of 6nm(side) cube.

I have defined a cylindrical region surrounding the CNT and having a thickness of 0.45 nm and length 6nm. So, I have some water molecules present in this region.

I want to perform vacf on the oxygen atoms present in that region surrounding the CNT. But, I am not able to form a group having only oxygen atoms which are present in that region.

In short my issue is that I am not able to define a group which will have a specific type of atoms present in a user defined region.

Thankyou.

2

Dear All,

I am trying to study the interaction between water and CNT through MD and have a simulation domain of 6nm(side) cube.

I have defined a cylindrical region surrounding the CNT and having a thickness of 0.45 nm and length 6nm. So, I have some water molecules present in this region.

I want to perform vacf on the oxygen atoms present in that region surrounding the CNT. But, I am not able to form a group having only oxygen atoms which are present in that region.

In short my issue is that I am not able to define a group which will have a specific type of atoms present in a user defined region.

Define a group that has all atom in that region, then a group that has all atom of the desired type and finally the group you want is the intersection of those two groups.

Axel