[gmx-users] gen_vel error

[Mark Abraham]

On 16/03/2010 12:28 AM, 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

If em.mdp is for energy minimization, then this is immaterial. This kind 
of mismatch is why we prefer to see input lines copied from your script 
or terminal to your email, not filtered through your head. People's 
heads are fallible!

> So is my simulation correct or does it generate velocities each time?
>
> I mean, what is meaningful: gen_vel or grompp -t -e ?

Generation over-rules those supplied to grompp.

With GROMACS 4, the use of checkpoint files should be preferred. grompp 
and mdrun the EM, grompp and mdrun the equilibration, and then grompp 
for the simulation without bothering with -t or -e, since they never 
preserved all the state variables anyway... Then supply the 
equilibration checkpoint file as input to the simulation mdrun and you 
can have no problems with continuity.

See webpage for more details on checkpointing and such.

Mark