[gmx-users] trjconv -pbc

Mauricio Pablo Sica msica at unq.edu.ar
Thu Jun 21 21:01:58 CEST 2007

> 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.

I have best resutls when using try '-fit rot+trans' in combination with 
'-pbc nojump'. If this is useless, I generate a new starting topol.tpr 
where the monomers are in the same cell and rerun the simulation. Then, 
trjcovn with '-fit rot+transand -pbc nojump'.

Good luck

> Belquis

Dr. Mauricio P. Sica                    LEPP
Phone: (54011)4365-7100 ext. 169        Laboratorio de Expresión
R. Saenz Peña 354                       y Plegado Proteico
(B1876BXF) Bernal, Buenos Aires         Universidad de Quilmes

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