[gmx-users] energy

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 6 01:38:38 CEST 2009

jayant james wrote:
> Hi!
> I ran a simulation for 1ns and I find that the energy file has been 
> written only till 627 ps. I am wondering how to extend my simulations  
> as I need the energy file (simulated with 1bar pressure)!!!
> I wonder why this is happening on a consistent basis. I cannot think of 
> the energy file being large nor the operating system not being able to 
> write it, because the .trr file is much larger than this file and is 
> being written down succedfully till 1000ps.  I am using GMX 4.0.
> I welcome any suggestions on how to extend the MD run and to overcome 
> this energy file problem.

You should be running version 4.0.4, and either way using checkpoints 
for your restarts. There's no GROMACS-related reason why your energy 
file should stop being written. It's rather more likely you or your 
filesystem have done something to cause the observations, but we can't 
tell what on this information.


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