[gmx-users] trjconv -pbc?

[bmmothan at ucalgary.ca]

Hello all,

I have tried using trjconv -pbc(all options) to get a continuous
trjactoary visulations on VMD.  I am modeling an 11 residue receptor
antiparellel to itself and one of the receptor strand jumps outside the
box sometimes.

I have used search to solve the problem but everthing i tried didnt work
and the -pbc just makes it worse.

I tried using the -pbc nojump alone and this made my two receptor strands
away from each other all the way (one inside and one outside the box).
However i want them to be close together since they are hydrogen bonded.

I have also tried: nojump then whole; whole then nojump and they make the
receptor just fly around or pieces of it stretch.

anyhelp is appreciated.

Belquis