[gmx-users] about the time of rerun

[K.A. Feenstra]

xu yechun wrote:
> 
> Dear all,
>     I use "mdrun -s file.tpr -rerun file.trr -e file.edr" to calculate the energy of one trajectory. It is surprising that
> the time for this process is almost the same as original process"mdrun -s file.tpr -o file.trr -e file.edr". Is it normal?I
> get confused.

As David said, it depends on how often you wrote a frame from your
original simulation. If you write a frame each step, each of them
will have to be re-evaluated, and that takes just as long as the
simulation took in the first place.

Disk I/O can be limiting, but if you use -rerun to calculate interaction
energies between a large number of separate groups (i.e. energy groups),
that can also slow things down considerably, mainly due to memory I/O.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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