[gmx-users] Frequency confout is updated

Mark Abraham Mark.Abraham at anu.edu.au
Wed Dec 16 16:07:56 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.

Not slowing things down significantly is only going to be possible when 
GROMACS can use a processor that isn't going to get interrupted. I'd 
recommend refreshing such a screensaver only every 30 seconds or so 
unless you're intending to run only on one core of multi-core machines. 
Obviously, test your mileage. The user isn't going to see much action on 
a desktop machine, anyway.

> 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

As Justin pointed out, these .mdp options refer to the -t trajectory 
output, and the -c structure file only receives the final configuration.

There's something to be said for you copying the -c mechanism and 
applying it every few thousand simulation steps to your own intermediate 
output structure file. The screensaver can simply poll that file.


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