[gmx-users] Re: Water models and diffusion coefficient

[David van der Spoel]

On 2013-02-09 19:26, learnmd wrote:
> For a simulation that is 300 ns long (after NVT and NPT equilibration steps
> of 1 ns each), I am saving output every 2 ps. The time step is 2 fs.
>
> nstxout         = 1000          ; save coordinates every 2 ps
> nstvout         = 1000          ; save velocities every 2 ps
> nstxtcout       = 1000          ; xtc compressed trajectory output every 2
> ps
> nstenergy       = 1000          ; save energies every 2 ps
> nstlog          = 1000          ; update log file every 2 ps
>
> Is that saving data too rarely?
>
No but check the flags in g_msd. Try without restarting, that is 
-trestart 300001.

> Thanks,
>
>
>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/Water-models-and-diffusion-coefficient-tp5005377p5005385.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se