Jack Shultz wrote:
I guess I misinterpreted the description. I take it there is no built
in mechanism to periodically write the structure.
There is :-) Trajectory output and checkpoint output.
Maybe I could revise
the source code to write the structure at every checkpoint?
Sure. That's what I was suggesting with my final comment. Find the
output mechanism that is used by -c and adapt it for use at the checkpoints.
Mark
On Wed, Dec 16, 2009 at 10:07 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote:
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.
Mark
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