The nvt time is too long

User discussions
1

Hi
good day
The nvt time is too long, in fact, the nvt file was not created until 40 minutes.
My protein is a homology model.
Can you help me, where is the problem of my work?
thank you

2

I’m sorry. I don’t understand what you mean. Do you mean that it is taking too long to run the NVT equilibration stage? That 40 minutes is too long for you for that stage? How do you decide what is too long? Or do you mean that it is taking 40 minutes to generate the NVT equilibration TPR (simulation input file)? In that case something is strange.

There are a few things you could consider regarding the simulation time:

  1. Is the NVT equilibration longer than necessary? Monitor (using `gmx energy) the temperature and, e.g., potential energy during the NVT equilibration. If these values seem stable long before the simulation has reached its end, you can probably shorten the simulation a bit.
  2. Are you using your hardware, such as GPUs, properly?
  3. What version of GROMACS are you using? Newer versions are often, but not always, more performant.

Finally, it is difficult to estimate what is a reasonable time to expect the NVT equilibration to take. It can range from a few minutes to many hours depending on the size of the system.

3

Hi
Thank you for your time
Yes GPU is working properly. GROMACS version is 2024
This step does not take much time for other proteins with almost the same number of amino acids…
But it takes too long for this homology model.

4

If you are using the same hardware, the same mdp parameters and the number of atoms (not only the number of residues) in the systems are similar, I would expect the run time to be similar as well.

Could you provide a bit more details, please? It is very difficult to help you based only on your very brief posts.