Dear Developers and Users,

Recently I wanted to simulate a solid system with a region of atoms fixed. I'm wondering if I want to use NVT to control the system temperature at 300K, should I include the fixed atoms as well? If I exclude the fixed atoms, will they be counted in the force calculations? Thanks!

fix NVT all nvt temp 300 300 0.01

OR

fix NVT mobile nvt temp 300 300 0.01

Bo

Dear Developers and Users,

Recently I wanted to simulate a solid system with a region of atoms

fixed. I'm wondering if I want to use NVT to control the system

temperature at 300K, should I include the fixed atoms as well? If I

better to not include the non-moving atoms.

exclude the fixed atoms, will they be counted in the force calculations?

yes, they will be included in the force calculations.

axel.

Thanks for your reply! Just want to make sure, if I use NVE and exclude the fixed atoms, will they be counted in the force calculations? Thanks again!

Bo

Thanks for your reply! Just want to make sure, if I use NVE and exclude the

fixed atoms, will they be counted in the force calculations? Thanks again!

you have to be more specific in what you mean by "exclude".

in general, when a force calculation is requested, all forces

that act on the group of atoms selected for time integration

are calculated with two special considerations:

- if you use r-respa, different force contributions are (re-)

computed according to their respa level

- the non-bonded force calculation is based on neighbor lists.

any manipulation of these - either via direct exclusion or

special bonds scaling factors - reflect on which pairs are

considered for the force computation.

if you have doubts about this, i recommend to build some

tiny test systems and write all positions, velocities, and forces

for a few steps and then manually check if the result is what

you expect. depending on how complex your input is, it may

be impossible to describe what is happening in general terms.

axel.

What do you mean by "counted in the force calc"?

NVE doesn't do any force calculations.

Steve