[gmx-developers] timestamp rounding in xtc

[Whitford, Paul]

GMX Developers,
I have a long simulation, and I noticed that at some point the timestamp in the xtc file gets rounded.  For sufficiently long simulations, this leads to many frames having the same timestamp. Here is a sample output from g_dist

15689440.0000000    4.1125884   -0.8720000   -3.9099998    0.9300003
15689441.0000000    4.0926588   -0.8410001   -3.8730006    1.0209999
15689441.0000000    4.0091296   -0.8900001   -3.7840004    0.9809999
15689442.0000000    3.9852955   -0.8520000   -3.7909999    0.8860002
15689443.0000000    3.9080644   -0.8450000   -3.6969995    0.9440002
15689443.0000000    3.8975551   -0.8559999   -3.6749997    0.9760003
15689444.0000000    3.9498629   -0.8680000   -3.7300005    0.9670000
15689444.0000000    3.9664337   -0.9370000   -3.7350001    0.9510002


I then use g_energy for the edr file from the same run:

15689440.200000  -68.322456
15689440.800000  -24.153179
15689441.400000  -172.497147
15689442.000000  -143.456650
15689442.600000  -225.489212
15689443.200000  -185.056137
15689443.800000  -192.895752


I checked gmx_dist.c, and it appears to not be performing any rounding, so it looks like the timestamp is rounded before it is saved to the xtc. Though, perhaps I am misunderstanding the code.

Additionally, when I run gmxcheck on the xtc file, I get many errors, similar to:

Reading frame       0 time 15689440.000
Reading frame       2 time 15689441.000
Timesteps at t=1.56894e+07 don't match (1, 0)
Reading frame       3 time 15689442.000
Timesteps at t=1.56894e+07 don't match (0, 1)
Reading frame       5 time 15689443.000
Timesteps at t=1.56894e+07 don't match (1, 0)
Reading frame       6 time 15689444.000


In later runs, this gets worse, and it appears to round to the nearest 2 ps, and not 1 ps.

These errors seem consistent with my impression that the timestamp is rounded before it is saved to the xtc.

Is there a need for this rounding?  I'm having trouble finding the source of it, so I'm also not sure how to disable it.  If you can point me to the right lines, that would be great.

Your help is much appreciated.

Paul Whitford

-------------------------------------------------------
Paul Whitford, Assistant Professor
Department of Physics
Dana Research Center, Room 123
Northeastern University
Boston, MA 02115
Office: 617-373-2952
Email: p.whitford at neu.edu<mailto:p.whitford at neu.edu>

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