[gmx-users] question about .trr file

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 10 17:40:27 CET 2009

Anna Marabotti wrote:
> Dear all,
> at present, when I'm doing a simulation (with Gromacs 3.3.3), I'm keeping both .trr and .xtc files, the first
> one in case of a continuation of the simulation, and the second one for analysis. As I saw in the manual and
> in the gmx-users list, the .trr file is essential for an EXACT restart of the trajectory since the program
> tpbconv reads coordinates and velocities in full precision, and the file .xtc does not contains velocities,
> and coordinates are in reduced precision. But file .trr is also a HUGE file when trajectories are very long.
> So I'm asking: how many steps are needed to correctly restart a simulation? For example, let's say I have to
> do 100 ns simulation. I'm obtaining my huge 1st.trr file. Then, I continue the simulation for 1 ns, and I will
> obtain the 2nd.trr file (smaller than 1st.trr, I suppose). Then, if I want to continue for other 100 ns
> simulation, can I use the 2nd.trr file with tpbconv to produce the new .tpr file, and will the final result be
> the same as if I use the 1st.trr file with tpbconv and continue the simulation for other 101 ns? If the answer
> if yes, I could store only the 2nd.trr file and delete the 1st.trr file, with a lot of space savings. Am I
> correct? 

What I typically do is dump off the last frame of the .trr when I've run a chunk 
of simulation time (trjconv -dump).  If the simulation runs to completion, say 
at 10 ns, and you want to pick it up from there, then there is no need to keep, 
for example, information from 5.5 ns; the latter is useful in case of a crash.

In your case, you could probably just keep 2nd.trr; once you are comfortable 
with doing restarts (which can also be accomplished by grompp), you can run 
shorter intervals of time to more effectively manage disk space.

Otherwise, you can simply reduce the output frequency of the .trr if you do not 
need to analyze velocity information (i.e., output every few hundred ps).  This 
will also save a lot of space.


> Thank you and regards
> Anna
> ______________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Skype: annam1972
> E-mail: amarabotti at isa.cnr.it
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
> ____________________________________________________
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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