[gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1

[Mark Abraham]

1ns is rather an eyeblink, and MD is chaotic... what is your evidence
that the trend of RMSD either run is representative?

Mark

On Fri, Aug 2, 2013 at 5:50 PM, Guillaume Chevrot
<gchevrot at cnrs-orleans.fr> wrote:
> Hi,
>
> I performed 2 simulations of a lysozyme in water: one with the version 4.5
> of Gromacs and another with the version 4.6.1 (I used the exact same
> inputs).
>
> Then I calculated the MSD and I obtained a complete different behavior with
> the version 4.6.1 of Gromacs and this MSD is obviously wrong.
> <http://gromacs.5086.x6.nabble.com/file/n5010317/MSD_gmxList.jpg>
>
> Do you have any ideas what I am doing wrong or did you encounter such a
> behavior?
>
> Regards,
>
> Guillaume
>
>
>
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