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

[Justin A. Lemkul]

Ramachandran G wrote:
> 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?

It seems like you're trying to extend your run using both grompp and tpbconv, 
which is not correct.  Use one or the other.

If you want a real answer to this question, please post real commands, not just 
the generic format of what should be correct.  Also possibly useful is the 
contents of the .mdp file you used.

-Justin

> Thank you
> Rama
> 
>  
>  
> 
> 
> 

-- 
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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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