> 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 Argentina ________________________________________________________________ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
