[gmx-users] gromacs with v-rescale thermostat

[Mark Abraham]

Hi,

Indeed, we changed this behaviour for 5.0 (and noted it at
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x)

Mark

On Sat, Dec 19, 2015 at 1:00 AM <michal.kolar at marge.uochb.cas.cz> wrote:

> Dear users,
> recently I have observed a strange behavior of my simulations. The total
> potential energy of presumably independent simulations showed undesired
> correlation (R=0.6) even when started with different velocities
> (gen-seed=-1) and solute coordinates.
>
> I found out that the reason is the v-rescale thermostat, which uses random
> numbers seeded by the ld-seed option in the mdp file. Unfortunately in
> gromacs 4.5 and 4.6 series, the default value is 1993, which causes the
> interdependence of the trajectories.
>
> The solution is to explicitly set ld-seed = -1 everytime the v-rescale
> thermostat is used. This is also the default value in gromacs 5+ versions.
>
> Hope this helps.
>
>
> with best regards
>
>
> Michal
>
>
>
>
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