[gmx-users] .trr file

[Mark Abraham]

Low Soo Mei wrote:
> Hi all,
> 
> I am quite new to Gromacs and would like to ask why the full _restart_ 
> file .trr  is designed such that every frame's coordinates and 
> velocities are retained? 

It only does this if you choose to do this. See discussion here 
http://wiki.gromacs.org/index.php/Doing_Restarts

> In NAMD and Amber only the last frame's 
> coordinates and velocities are necessary for a restart.  I mention this 
> because am wondering why it appears that the full .trr file is read when 
> grompping for my continuation run.

Yes, they're all read, but that's only expensive if you choose it that 
way - and even then it's not much.

> Unless the Gromacs analysis tools also use the .trr file for analysis, 
> in which case keeping data for every frame in the .trr makes more sense.

There are occasions for wanting velocities and forces over the 
simulation. GROMACS allows you to decide in advance what you'll want and 
to be efficient accordingly.

Mark