[gmx-users] t_trxframe speed units

Berk Hess gmx3 at hotmail.com
Thu Sep 3 18:17:06 CEST 2009


The only thing I suggested was using pull_start=yes,
otherwise you will start at a "random" distance and you will have enormous  forces.
Did you try that?

Do you have a rectangular or a triclinic box?


> Date: Thu, 3 Sep 2009 18:00:44 +0200
> From: alexander.herz at mytum.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] t_trxframe speed units
> Hey,
> I tried everything you suggested and a couple more things and still it
> is not possible to get a reasonable speed
> for the pulled groups (always way beyond the 0.01nm/ps set in the mdp
> file and mostly containing some high frequence patttern probably related
> to pbc). (I tried: constraint, pbcatoms, direction,position and using no
> ref group).
> Can I send you a small sample system with the problem or is there
> something else I can do?
> Thx,
> Alex
> Berk Hess schrieb:
> > But you can not talk about popping back, since there is pbc.
> > What matters is how the pull code determines the distance.
> > At least in 4.0.4 and 4.0.5 it add the rate*t before doing pbc,
> > such that it pulls smoothly even if the distance is larger than the box

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