[gmx-users] trjconv -pbc

[Rainer Boeckmann]

you could test it. just apply tpbconv on the trajectory to get a new tpr-file,
or the trjconv -pbc whole/nojump procedure on the first 20ps. 
cheers,
rainer

-------------------
> 
> 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
>