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

Mark Abraham mark.j.abraham at gmail.com
Sun Apr 22 16:00:22 CEST 2018


All GROMACS tools have the units described in chapter 2 of the reference
manual as basic assumptions. If you supply a trajectory that means
something other than say 12.1 ps when writing a time of 12.1 for a
trajectory frame, then you will need to remember that when you go to
interpret your results. So you need to go and find out what that other tool
writes (e.g. look at its docs, or use gmx dump -f if you have to).


On Sat, Apr 21, 2018 at 9:18 PM jt555 <jt555 at protonmail.com> wrote:

> 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.
> Sent with [ProtonMail](https://protonmail.com) Secure Email.
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