Is it possible to transfer heat from one group to another using simulated aneeling technique in the Gromacs software? I would like to transfer heat from a gold nanoparticle (group 1 from 310 to 350 K) into a dppc bilayer (group 2) that is at 310 K. How can I do it using a NPT ensemble in a molecular dynamics?
I was recently looking for the answer of a related question: is there any way we can calculate thermal conductivity in GROMACS? I couldn't find the solution.
The closest thing I manage to do was to define several groups according to some criteria (let's say the distance to an interface) and apply each group a single thermostat.
So, I think you should define a group that will not be under the action of any thermostats and two other groups that are subjected to different thermostats with different temperatures that would work as thermal reservoirs.
Hi Andre, According to https://manual.gromacs.org/current/reference-manual/algorithms/simulated-annealing.html one has to design a dynamics script to perform the SA in GROMACS. I guess the idea is to take the group-1 (nanoparticle) with a T1 as parameter in the script and T2 (given and constant) for the lipid. You only need to run MD for some time (τ) in order to relax your system and then restart your MD protocol proceed the iteration. Let me know if it helps.
Dear Adolfo, thanks. This was our first try. It does not work at all.
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics