[gmx-users] question about .trr file

Anna Marabotti anna.marabotti at isa.cnr.it
Tue Feb 10 15:45:07 CET 2009

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
Thank you and regards
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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