[gmx-users] Disk Space
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 14 22:10:30 CEST 2010
teklebrh at ualberta.ca wrote:
> 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.
Unless you need full-precision coordinates every few ps, you can use nstxtcout =
2000 and set nstxout = 0. A .xtc file is substantially smaller than a .trr file.
> 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.
>> 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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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