Default value of gen-vel option in gromacs MDP file

User discussions
1

Dear gromacs users,

I am using mdp files provided by charmm-gui webserver. The server provides mdp files for a position-restrained NVT equilibration followed by an NPT production run. The NVT equilibration mdp file contains gen-vel = yes, gen-temp = 303.15; however the production mdp file does not contain any gen-vel option. I would like to know if we don’t provide any option for gen-vel, does gromacs by default consider gen-vel = no and does not generate velocities? I checked the mdout.mdp file after running grompp and it shows gen-vel = no. Any explanation would be appreciated, thank you!

2

Generating velocities is only done during the first stage of equilibration. You don’t want to randomize velocities at any later point, because it obliterates the prior equilibration and now you’re starting from a random state. The jobs continue from checkpoint files that contain all the state information.

3

Thank you for your reply Dr. Lemkul. We should generate velocities only when we change temperature, is that so? also does keeping gen-vel = no in the mdp file is same is not providing gen-vel option at all in the mdp file? In the manual it is not mentioned about the default value/option for gen-vel.

4

You only need to generate velocities when there are none. You don’t have to regenerate them if you change the temperature using a thermostat, however, you might need some time to equilibrate the system to a new temperature.

In Molecular dynamics parameters (.mdp options) - GROMACS 2024.4 documentation it says “Default values are given in parentheses, or listed first among choices. The first option in the list is always the default option.” Looking at Molecular dynamics parameters (.mdp options) - GROMACS 2024.4 documentation, the first option is “no”.

5

Thank you for your reply, I got the clairification. So even for a replica-exchange MD we don’t need to regenerate the velocities at each temperature.

6

OK. I didn’t know you meant for replica exchange. In that case you want to generate velocities for each replica when you equilibrate since you want the states to be different.