[gmx-users] gen_vel error

[Justin A. Lemkul]

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:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

-Justin

> Thank you
> Carla
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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