[gmx-users] Frequency confout is updated

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 17 02:37:07 CET 2009

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.


> On Wed, Dec 16, 2009 at 10:07 AM, Mark Abraham <Mark.Abraham at 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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