[gmx-users] Frequency confout is updated

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 16 15:51:39 CET 2009

Jack Shultz wrote:
> Hello,
> I would like to setup a screensaver to visualize structures as we are
> simulating them. We want to avoid slowing down the simulation
> significantly. I found a solution that read pdb files. Is there a way
> to reduce the frequency mdrun updates the confout.gro?
> The structure file (-c) contains the coordinates and velocities of the last step
> -c  confout.gro  Output  Structure file: gro g96 pdb
> if I increase these values, does it write to these files less
> frequently or are we stuck with the updating this structure every
> step?
> nstxout: (100) [steps]
> frequency to write coordinates to output trajectory file, the last
> coordinates are always written
> nstvout: (100) [steps]
> frequency to write velocities to output trajectory, the last
> velocities are always written

The confout.gro file is the last output of mdrun; it is written once (hence 
"coordinates and velocities of the last step") and thus is unaffected by nst* 
options, which only affect the trajectory.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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