[gmx-developers] do_update_md

[Mark Abraham]

Hi,

That looks like a bug that was silently fixed during the adoption of the
velocity-rescale thermostat of Bussi (see commit
333641e040ae824badf9d9531290a46ad581ed53). It may be that the issue wasn't
noticed because people often used parameters that produce lg == 1...

I would strongly advise avoiding doing development work on unsupported
versions of the software more than five years old... ;-) Get the git master
branch and stay up to date with the hundreds of bugs that have been fixed
since :-)

Mark

On Fri, Jun 9, 2017 at 2:01 PM Zachmann, Martin <m.zachmann at tum.de> wrote:

> Hello community!
>
> i hope someone can help me understand some code changes in the
> do_update_md() function in update.cpp.
>
> In the case where it advances r and v in the leap-frog scheme together
> with the berendsen thermostat
>
> (last two else if { } and else { }) in version 4.0.7. it looks like this
>
> vv = lg*(vn + f[n][d]*w_dt);
>
> where lg is the lambda-scaling factor from the thermostat and w_dt is dt/m.
>
> Instead in version 4.5. and higher:
>
>  vv = lg*vn + f[n][d]*w_dt;
>
>
> The original paper (The Journal of Chemical Physics 81, 3684 (1984); doi:
> 10.1063/1.448118) seems to scale
>
> both old velocity and force. Btw in do_update_visc() scaling is done to
> both.
>
> What is the purpose of this?
>
> any help is much appreciated,
>
> regards Martin
>
>
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