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.ne...@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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