Shyno Mathew wrote:
Dear all,
This is the first time I am trying to extend a run in gromacs.
I read in the gromacs website following are the steps to used for this
purpose:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
So this means I don't need to modify the .mdp file at all?
Correct.
For instance, what about these two parameters: tinit, continuation
I thought tinit has to be changed to time last time step of previous run
and continuation has to be set to 'yes'.
The only time you have to use .mdp files for continuation is if you are changing
some aspect of the ensemble, output control, etc. Tutorials have you deal with
the continuation parameter, for instance, when moving between different steps in
equilibration. That is because you are changing the ensemble (NVT, NPT, etc)
and thus you cannot do a simple extension of the simulation. For production
simulations that simply require more time, the steps listed on the Gromacs
website are correct and there is no need to deal with .mdp files.
-Justin
--
========================================
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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