Juliette N. wrote:
Hello all,
I read the online instruction on how to extend a run. I just wanted to
double check the procedure because of the NOTE below after issuing
tpbconv –f old.trr -s old.tpr -e old.edr -o old-extend.tpr -until 10000
NOTE: Reading the state from trajectory is an obsolete feaure of tpbconv.
Continuation should be done by loading a checkpoint file with mdrun -cpi
This guarantees that all state variables are transferred.
tpbconv is now only useful for increasing nsteps,
but even that can often be avoided by using mdrun -maxh
Modifying ir->bContinuation to TRUE
NOTE: The simulation uses pressure coupling and/or stochastic dynamics.
tpbconv can not provide binary identical continuation.
If you want that, supply a checkpoint file to mdrun
------------------------------------------------------------------------------
then used cpi option to include checkpoint file :
mdrun -deffnm old-extend -s -o -c -g -e -x -cpi old.cpt
Am I doing things correctly?
As implied by the note, the -f and -e flags and the files they provide are
unnecessary. The checkpoint file guarantees a correct continuation. The exact
commands you need (substituting -extend or -until, whichever you prefer, though
-until is a bit more reliable where rounding is concerned) are here:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4
-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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