[gmx-users] Request on initial velocities

Mark Abraham mark.j.abraham at gmail.com
Fri Nov 11 18:56:56 CET 2016


The vv integrators write velocities on the full step, but those in the .tpr
file are interpreted as occurring on the previous half step (which is
consistent with how the leap-frog integrators start up). So a half-step of
integration (ie. of velocities) takes place before any trajectory output is
written. For vv, all the trajectory output is on-step. For leapfrog,
positions are on step and velocities trailing by a half step.


On Fri, Nov 11, 2016 at 5:59 PM Riccardo Conte <riccardo.conte1 at unimi.it>

Dear Gromacs users,

I am experiencing an issue in trying to perform a dynamics run by feeding
in my own starting velocities. My procedure is as in the following:

1) I build my .gro file with the desired starting position and velocities;
2) I choose the flag "no" for the "gen-vel" option in the .mdp file;
3) I run my dynamics with the md-vv-avek integrator because I am interested
in a NVE simulation (no thermostat).

Once I get the outcome of the dynamics run, I can notice that the
velocities at the initial step are different from those I passed to the
Is there a way to fix this issue? Am I wrong in one of the previously
listed steps?

Many thanks,


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