dump_modify unwrapped

Dear All users,

I’ve just performed a simulation and recorded the coordinates of centre of masses of my

molecules but some of them are out side of my box. I have check the manual. It means that I

should use No for dump_modify unwrapp command for having coordinates in our boundaries. Am I

right?

Dear All users,

I've just performed a simulation and recorded the coordinates of centre of
masses of my

molecules but some of them are out side of my box. I have check the manual.
It means that I

should use No for dump_modify unwrapp command for having coordinates in our
boundaries. Am I

right?

no.

Dear Axel,

I was a bit confused, in VMD when I want to watch my traj files I do wrapping for having a simulation box including atoms with logical

coordinates. How can I solve my problem by unwrapping yes?

Dear Axel,

I was a bit confused, in VMD when I want to watch my traj files I do
wrapping for having a simulation box including atoms with logical
coordinates.

this is an even more confusing statement. what are "logical
coordinates" and what has viewing trajectories to do with compute
com/molecule?

How can I solve my problem by unwrapping yes?

you have not defined what "your problem" is?

as far as i can tell, your problem is that you have too many questions
and too few answers and *that* cannot be solved through unwrapping.
:wink:

axel

Dear Axel,

I recorded My COM’s coordinates whit this command com/molecule and ave/time. My COM’s coordinates reveal that I have a system with larger box. I can

find them beyond my system boundaries.

How can I have COMs in my simulation box without going out of my box?

Dear Axel,

I recorded My COM's coordinates whit this command com/molecule and ave/time.
My COM's coordinates reveal that I have a system with larger box. I can

no. you don't. you have a *periodic* box. so (part of) molecules leave
the *principal* box.

find them beyond my system boundaries.

How can I have COMs in my simulation box without going out of my box?

you cannot. where is the problem?
you need to apply PBC to your results anyway.
if you would ignore PBC for your atoms, you would get totally
unphysical results. the COM of a molecule half outside, half inside
the principal simulation cell would bit in the center of the cell and
that would be totally wrong.

axel.

p.s.: and here we have *another* case of not thinking and not solving
a problem, but just insisting and asking.

Dear Axel,

Thank you very much for your reply.