[gmx-users] trjconv -pbc

[Andre Farias de Moura]

hello again,

there is a gap between my tpr-file and the trajectory,
my tpr-file was generated from the first structure, before
any energy minimisation or heating was performed. but I do
not think this gap is so wide, it's just a 20 ps run before
the simulation starts. and the frames are not so far away
from each other, I've chosen frames in the range of 1-5 ps,
but it doesn't matter, I allways end up with two or three
broken lipids. the only mistake I have noticed is that my
starting configuration had an aggregate near the box edge,
so that lipid molecules began to jump across the interface
at the very heating step. could that be the reason trjconv
cannot handle my trajectory as it should?

thanks again,

andre

On Tue, 11 Mar 2003, Rainer Boeckmann wrote:

> trjconv -pbc nojump starts indeed with the coordinates of the
> tpr-file. Therefore you end up with broken molecules if the time gap
> between tpr-coordinates and coordinates of the first frame of the
> trajectory is too large. (I wouldn't call it a bug, it is even
> useful.) rainer
>
> Anton Feenstra wrote:
>
> > Rainer Boeckmann wrote: > > Hi Andre, > > > > do you apply -pbc
> whole/-pbc nojump on the whole trajectory or only on snapshots > > or
> parts of the trajectory (with the initial tpr-file)? In the latter
> cases you > > might get broken molecules due to a change in box vector
> length. The nojump-flag > > uses the box parameters from the
> trajectory and not from the tpr-file. A > > solution would thus be to
> apply the procedure with whole & nojump on the whole > > trajectory
> (or on a small part with a changed tpr-file). trjconv -pbc nojump > >
> uses the tpr-file coordinates as a reference for the first frame but
> the box > > parameters from the first frame of the trajectory. > >
> That doesn't sound quite right. If that is really the case, it might
> be a bug. > Can someone look into that? > > -- >
>
> --
> Dr. Rainer Böckmann
> Theoretical Molecular Biophysics Group
> Max-Planck-Institute for Biophysical Chemistry
> Am Faßberg 11
> D-37077 Göttingen
>
> tel:    +49(551)201-1141
> mobile: +49(172)9531168
> fax:    +49(551)201-1089
>
> email: rboeckm at gwdg.de
>
> http://www.mpibpc.gwdg.de/abteilungen/071/rainer/index.html
>
>
> ‚ln±ê왨¥Šx%ŠË`›¬z» ®‰šrÊ+‚m§ïÿÃ ®‰šrÊ+ƒùšŠYšŸùb²Ø§~à›¬z»•æ¬yÚ'¶š,¶éì¹»®&Þ­ê®zËl¶‹azX¬µK¶°Ã§µêßiǨ®Ç§v+m¢	±ºÇ«²·ª¹ë-‚º&iË(®