[gmx-users] Re: rerun of trajectory

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed May 14 23:56:01 CEST 2003

>actually the trr file is about 5.3G.its really huge as i have
>saved the velocities every 0.2ps.also i ran the tpbconv command from the
>same dir which has the .trr file.But it still does not seem to recognize
>will increasing the number of steps after which the velocities
>are written help me decrease the size,say after every 10 or 15ps.

There are a couple of things you can do to decrease the size of the 
trajectory file that is written out by mdrun.
         1/ save the position and velocities to .trr less often.  How often 
you need it depends on what you want to do with the information.
         2/ use the .xtc file format for saving your trajectory.  This file 
format is much smaller than .trr
         3/ if you use the .xtc file format then you don't have to save to 
..trr very often at all, only really the final step if you want to extend 
the simulation.  This can be wasteful though, as if your simulation crashes 
somewhere then you have to start from the very start again and there can go 
a significant amount of CPU time.  Personally I have mine save every about 
6 hours real time and only keep the last .trr file so if the need arises I 
can continue the simulation.  Everything else is saved and archived as .xtc

>i have a feeling the huge memory size of 5.3.g for only 1ns seems to be giving
>me the trouble. i'm unable to view the movie also in VMD.Also my system is
>quite huge,about 22500 atoms.

Couple of things you can do here as well.  Convert the file to .xtc, that 
will divide the file size again by about 3.  Using trjconv remove all the 
atoms that are not of importance to see from the trajectory, such as may be 

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.

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