On 5/28/12 3:49 PM, rama david wrote:
Thank you Justin for reply...
More or less. The special case with what you're doing in the tutorial is
that you have no initiating velocities in each window; you only have
coordinates. That's why it makes sense to do a bit of equilibration in each
window first, generating velocities and re-equilibrating the system.
-Justin
In npt_umbrella.mdp we have
gen_vel = yes
The command line in tutorial is
grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr
...
grompp -f npt_umbrella.mdp -c conf450.gro -p topol.top -n index.ndx -o npt22.tpr
So if I modify the process as follow, Then is the need of equilibration (Can we
skip equilibration and run production md)
use -t flag with cpt ( to give velocity of the previous run ) file
continuation = yes
gen_vel = no .
Is these alternative process is right or totally wrong..???
Using the checkpoint in this instance is wrong. The only checkpoint you have
accessible to you at that point is from the end of the pulling simulation and
corresponds to the final state of the system. Applying these velocities to the
intermediate configurations along the reaction coordinate is likely to do weird
and unreliable things to the trajectory. It is more robust to run NPT and then
data collection, or as I said before, proceed immediately to a continuous data
collection (with gen_vel = yes!) and discard the initial few ns of data as
equilibration. In theory, this procedure is no different than any other
simulation that one conducts.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
