[gmx-users] Re: on the trr file of the production MD

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 10 00:20:44 CEST 2012

Acoot Brett wrote:
> Dear All,
> I have a practice on the production MD according to the on-line lysozyme 
> tutorial of *Justin Lemkul 
> *(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html). 
> By the production MD step, I got 2 .trr file, one is md_0_1.trr, the 
> other is traj.trr file. I think these 2 files are same, am I right?

One run should not produce two .trr files, and certainly not with different 
names.  Check to make sure you do not have two different invocations of mdrun 
running.  If you're following the tutorial, traj.trr will arise if you do not 
supply the -deffnm flag to mdrun, since traj.trr is the default output file name.

Do not assume that md_0_1.trr and traj.trr are the same.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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