msd

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1

hi dear dr. Kohlmeyer

thanks for your reply . I want to get all of my atoms fixed ( without any moving) during simulation , except the molecules that i want to compute their msd . for this what command should i use .

thanks
best
ramin

2

hi dear dr. Kohlmeyer

thanks for your reply . I want to get all of my atoms fixed ( without any
moving) during simulation , except the molecules that i want to compute
their msd . for this what command should i use .

just don't include the "fixed" atoms in the time integration.

but i don't understand the strategy. are the other atoms
not moving in reality?

in any case, particularly this topic has been discussed TO DEATH
many times on the mailing list. search through the archives and
read the HOWTO section of the manual.

in general, a _lot_ of "how do i set up ....?" questions are
recurring, so a search through the mailing list archives
is always recommended. ...and i would not stop at the
first matching answer, since there are often several
approaches to do the same thing and sometimes one
has advantages over the other.

axel.