[gmx-users] Disk Space

[teklebrh at ualberta.ca]

Dear Chris,

Thank you very much!

I am planning to set the output control option like this!

tinit               =  0
nstxout             =  2000
nstvout             =  0
nstfout             =  0
nstlog              =  2000
nstenergy           =  1000

I want to set the velocity and force option to zero and save the  
coordinate and energy every 1000 or 2000 steps ( 2ps or 4ps). By doing  
this am I missing anything.

regards,

Rob



Quoting chris.neale at utoronto.ca:

> Dear Rob:
>
> To answer your question: just set up your run with nsteps for 5 ns,  
> run mdrun, and then use tpbconv -until. A simpler option is to set  
> it up to run 20 ns, but use -maxh to limit it to an amount of  
> runtime that you pre-calculate to be similar to 5 ns of simulation.
>
> HOWEVER:
>
> You almost surely don't need to save this so often: nstxout = 100  
> (also nstvout, nstfout).
>
> And you may not even need to save this so often: nstxtcout = 100  
> (also nstenergy).
>
> I had no idea that there was an option nstcheckpoint = 100 as I use  
> mdrun -cpt 6 to specify a .cpt file every 6 hours, but there is no  
> need to write a .cpt every 100 steps.
>
>
>
> Dear Gromacs users,
>
> I am running an MD simulation but it looks to me that I am running out
> of disk space.
>
> This is my .mdp file
>
> ; OUTPUT CONTROL OPTIONS
>
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout                  = 100
> nstvout                  = 100
> nstfout                  = 100
> ; Output frequency for energies to log file and energy file
> nstlog                   = 100
> nstenergy                = 100
> ; Output frequency and precision for xtc file
> nstxtcout                = 100
> xtc-precision            = 100
> nstcheckpoint            = 100 ; checkpointing helps you continue
> after crashe. This checkpint file is saved every 1ns
>
>
> Please tell me which files i need to set zero.
>
> I am planning to run my simulation for 20ns but I want it to run every
> five nanoseconds until i see an aggregations in my system. So how can
> I re-start my simulation every 5ns.
>
>
> Thank you for your help
>
> rob
>
>
>
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