[gmx-users] Frequency confout is updated

Jack Shultz js at drugdiscoveryathome.com
Wed Dec 16 18:04:33 CET 2009

I guess I misinterpreted the description. I take it there is no built
in mechanism to periodically write the structure. Maybe I could revise
the source code to write the structure at every checkpoint?

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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