Dear all,

I want to define the volume of a group. I tried to define it by the variable command but I found that volume cannot be define as mass(group_ID) which is used to define mass of a group. How can I define it?

Thank you.

ZQ Liao

Dear all,

I want to define the volume of a group. I tried to define it by the variable command but I found that volume cannot be define as mass(group_ID) which is used to define mass of a group. How can I define it?

Thank you.

ZQ Liao

Assuming you are working with an atomic representation.

The volume of a point particle is … ZERO!

Thus, the volume of a finite group of them is… ZERO AGAIN!!!

Carlos

You can use compute voronoi/atom to

compute volumes of neighborhoods around

particles, then sum the result with compute reduce,

for atoms in a group.

You do realize that “volume” of an atom, or a group

is an ambiguous quantity.

Steve

Take a look at the voronoi/atom compute. Used together with a 'reduce

sum' compute I can define the voronoi volume of a group. This might

work for you, if you are working with dense systems.

Daniel

Dear all,

I want to define the volume of a group. I tried to define it by the variable

command but I found that volume cannot be define as mass(group_ID) which is

used to define mass of a group. How can I define it?

what is the volume of a group of atoms? how would you define it in words?

is it the sum of the volume of the atoms? if yes, what is the volume

of a single atom? what happens if atoms overlap?

is it the volume of its enclosing surface? if yes, how to define the

surface? do you just connect the centers (positions)? or is it the

"accessible" surface? then how to choose the probe radius? don't you

have to consider the volume of atoms still?

how about "holes"? what is the volume of a vesicle? what would be the

volume if the group had just one atom?

there are lots of questions and ambiguities that make the computation

of a volume of a group of atoms non-trivial. different approaches can

be used for different cases and with different levels of accuracy. so

before asking for this again, please sit down and define for yourself

how you would define the volume of a group of atoms precisely and use

the questions from above as a guide. if you can answer those to your

satisfaction, you also have found the way how you can compute what you

are looking for.

axel.

Thank you. You helped me a lot. I have thought the problem too simply.

ZQ Liao

Dear sir

I realized the mistake I have made. How to get the quantity or total mass of a region but not a group?Thank you.

ZQ Liao

Dear sir

I realized the mistake I have made. How to get the quantity or total mass of

a region but not a group?