[gmx-users] extending the simulation with modified mdp option

Ramachandran G gtrama at gmail.com
Thu Jan 13 00:02:41 CET 2011


Hi gmx-users,
    I tried extending one of simulation with modified mdp option.
First i used the command,

> grompp -f new.mdp -c old.tpr -o new.tpr
then i used the command to extend
> tpbconv -s new.tpr -extend timetoextendby -o next.tpr
Then,
> mdrun -s next.tpr -cpi previous.cpt

I surprised to see the following simulation output,
WARNING: This run will generate roughly 2059394074917430016 Mb of data

starting mdrun 'GROningen MAchine for Chemical Simulation in water'
2000000 steps, infinite ps (continuing from step 12000000,   6000.0 ps).
step 12000000 performance: 0.3 ns/day
step 12000100 performance: 0.8 ns/day
step 12000200 performance: 0.8 ns/day
step 12000300 performance: 0.8 ns/day
step 12000400 performance: 0.8 ns/day
step 12000500 performance: 0.8 ns/day
step 12000600 performance: 0.8 ns/day
step 12000700 performance: 0.8 ns/day
step 12000800 performance: 0.8 ns/day
step 12000900 performance: 0.8 ns/day
step 12001000 performance: 0.8 ns/day
step 12001100 performance: 0.8 ns/day
--------------------------------------------------
Is this correct? Why it needs to generate that much huge Mb of data?
I have extended for 1000.0ps but it shows 'infinite ps'.
can anybody help me if there is error made in my procedure?
Thank you
Rama
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