[gmx-users] gen_vel error

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 15 14:36:35 CET 2010

Carla Jamous wrote:
> Hi everyone,
> Please I made an error during my simulation:
> I ran my simulation in the following way for many steps:
> grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top
> mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log
> But in my em.mdp,
> I kept: gen_vel = yes
> So is my simulation correct or does it generate velocities each time?

If you're telling grompp to re-generate velocities, then that's what it's going 
to do; the resulting trajectories will be discontinuous.

> I mean, what is meaningful: gen_vel or grompp -t -e ?

If you use -t and -e in conjunction with "gen_vel = yes," grompp will print a 
note saying that the supplied velocities are ignored and it is generating new 
ones.  Gromacs output tries as hard as it can to help you not make errors :) 
The proper way to extend a simulation can be found here:



> Thank you
> Carla


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list