[gmx-users] gen_vel error
Mark.Abraham at anu.edu.au
Mon Mar 15 14:42:01 CET 2010
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.
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