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 <[email protected]> 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
