[gmx-users] Fundamental Units of MDS Package (time unit t = 48.88821 femtoseconds)

jt555 jt555 at protonmail.com
Sat Apr 21 21:17:42 CEST 2018

Hello there,

I am writing to seek clarification regarding the fundamental units of a molecular dynamics package. In the manual it clearly states that the fundamental units are as follows:

Length Angstrom (0.1nm); Energy kcal/mol; Temperature Kelvin and Mass g/mol. Further these yield the derived units:

- time unit t = 48.88821 femtoseconds

I used a separate code for the simulation and am employing GROMACS version 5.1.2 to perform trajectory analysis. However, I am somewhat confused by the time unit of 48.88821 fs. I ran a microsecond-long simulation (~1000 ns) and the system (under investigation) equilibrated at 250 ns. However the output files (most notably the .xvg files) would suggest that the system equilibrated at 2.50e+08 picoseconds (= 250000 nanoseconds). If, however the figure above (2.50e+08) was expressed in femtoseconds, then there would be no confusion.

I would be most grateful for any comments you may wish to make regarding this matter.

Thank you in advance.

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