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
--
========================================
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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