GROMACS modification: Yes/No
Here post your question
I am trying to simulate crystallization of an ionic liquid on graphite at low temperatures (around 190 K). I am using GROMACS. How can I apply the low temperature condition in MD/GROMACS? And is this possible to predict crystal structure at low temperature using MD?
you can performed the simulation at low temperature by defining the desired temperature using the option ref-t in the mdp parameter files.
see more on thermostat definition
details on mdp parameters here
Thank you @alevilla ,
What I am trying to do is the unit cell structure of an ionic liquid. I prepared the .itp files for the anion and the cation, and also for the graphite substrate.
I tried the .gro combination and after that the .mdp file run for simulation, but I got too many errors which I don’t know what they mean.
Can you help me with the steps required to do the simulation? I can email you the files I created.
where do you get errors? In the pre-processing (gmx grompp) or gmx mdrun? During energy minimization or equilibration?
I fixed the errors. It is running now.
I am not sure if I can check if the simulation is working well now, or I have to wait until the last moment.
This simulation is at room temperature, and what I actually need is at lower temperatures, so I have to repeat the simulation at other temperatures as well.
I have one question at this point. If the size of the substrate plane is bigger that the size of the ionic liquid box I am using, is it affecting the simulation?
I attached the errors. And showed how the system looks like in vmd for the output when the simulation stop because of these errors.
Can you help me to solve this?
Yes that is a problem, all the particles (atoms) coordinates of the system should be inside to the defined box. From a visual inspection of VMD figure, looks like you have a box wider as the substrate.
What is the best way to reduce the substrate size?