[gmx-users] Disk Space

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Jun 12 00:00:03 CEST 2010

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.


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  

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 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


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