Velocity generation in the nvt, npt and md.mdp files

[M_Abdelaal]

GROMACS version: 2020.2
GROMACS modification: No

Hello everybody,

I am simulating the deposition of C60 molecules on a graphene sheet. My moelcules should have velocity and hence, I allowed velocity generation during the NVT equilibiration (I wrote in my nvt.mdp file generate velocity = yes). The question is, should I also allow velocity generation during the NPT equlilibration and the production run (velocity generation = yes in my npt.mdp and md.mdp files) ?

By using the generate velocity = yes in all my nvt.mdp, npt.mdp and md.mdp files, does this mean that I am generating new velocities in each step and ignoring the velocity generated from the previous step ?

[jalemkul]

@M_Abdelaal

GROMACS version: 2020.2
GROMACS modification: No

Hello everybody,

I am simulating the deposition of C60 molecules on a graphene sheet. My moelcules should have velocity and hence, I allowed velocity generation during the NVT equilibiration (I wrote in my nvt.mdp file generate velocity = yes). The question is, should I also allow velocity generation during the NPT equlilibration and the production run (velocity generation = yes in my npt.mdp and md.mdp files) ?

Don’t do this.

By using the generate velocity = yes in all my nvt.mdp, npt.mdp and md.mdp files, does this mean that I am generating new velocities in each step and ignoring the velocity generated from the previous step ?

Yes, exactly. You’re randomizing the system again, thus defeating the purpose of any prior equilibration.

[M_Abdelaal]

Thanks a lot :)