[gmx-users] Re: oscillations in constrain forces

[fangel at usc.es]

Hi Berk,
what means long time averages? between 0 and 5 ns the oscillations doesn't
decrease and the average value seems to be zero, in fact those oscillations
look like noise.. could be that the force I want to measure is too small?

Thanks for your help,

Ángel Piñeiro.


> Date: Mon, 21 Jun 2004 16:06:29 +0200
> From: "Berk Hess" <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] oscillations in constrain forces
> To: gmx-users at gromacs.org
> Message-ID: <BAY16-F48tvptvt4I9p000029e8 at hotmail.com>
> Content-Type: text/plain; format=flowed
>
> >From: fangel at usc.es
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: gmx-users at gromacs.org
> >Subject: [gmx-users] oscillations in constrain forces
> >Date: Mon, 21 Jun 2004 11:21:11 +0200
> >
> >Dear all,
> >I am trying to use the pull code to constrain the distance between the
> >center
> >of
> >mass of two molecules but I am obtaining very high oscillations (between
> >1000
> >and -1000) in the
> >output.pdo.
>
> These fluctuations seem quite reasonable to me.
> You need long time averages to obtain reliable values.
>
> >
> >A second question: Doesn't the pull code work in parallel? From the
mailing
> >list
> >it seems that it does not in previous versions but I do not know in 3.2
>
> All the pull code should work in parallel, except for constraint pulling.
> When you try this it will give a fatal error.
> If all constrained molecules are on node 0 it is easy to make the code
pull
> work in parallel.
>
> Berk.